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1

[Primary hiperoxaluria: a new mutation in gen AGXT (R197Q) cause of neonatal convulsions].  

PubMed

Primary hyperoxaluria is a congenital innate error of the metabolism of the amino acids, that is transmitted like an autosomal recessive character. Two types of hyperoxaluria exist: the primary type I, that corresponds to the peroxisomal enzymatic deficit of the alanine glyoxylate aminotransferase in the liver (AGT) and type II, due to the deficit of the glyoxylate reductase/hydroxypyruvate reductase deficiency (GRHPR). The primary type I (AGT) is the most frequenty. We report the case of a female infant of one month of age, that on her first day post birth, presented myoclonic convulsions and tonic spasms, both during wakefullness and sleep periods, that became more frequent and did not respond to the use of anticonvulsants. The ictal Electroencephalogram presented an intermittent activity of spikes and spike-waves of high voltage in the right hemisphere. Eight minutes after the intravenous administration of 150 mg of pyridoxine, it was observed a diminution of the epileptic activity, as well as the clinical manifestations. The determination of organic acids in urine revealed an increase in the concentration levels of oxalic acid (3064 mmol/mol of creatinine). The molecular genetic study of the AGXT gene, showed the existence of a R197Q mutation in exón 5 of the patient and her father. She received treatment with pyridoxine at a dose of 50 mg/day. When she reached the age of three months both a normal electroencephalogram and biochemistry were obtained. Although it is a rare cause of neonatal convulsions, hyperoxaluria, due to new mutations is an underdiagnosed disease by neonatologists and paediatricias. PMID:19245173

Guevara-Campos, José; Riverol, Débora; González-Guevara, Lucía; Tinedo, Rubin

2008-12-01

2

Selected AGXT gene mutations analysis provides a genetic diagnosis in 28% of Tunisian patients with primary hyperoxaluria  

PubMed Central

Background Primary hyperoxaluria type I (PH1) is a rare genetic disorder characterized by allelic and clinical heterogeneity. Four mutations (G170R, 33_34insC, I244T and F152I) account for more than 50% of PH1 alleles and form the basis for diagnostic genetic screening for PH1. We aimed to analyze the prevalence of these specific mutations causing PH1, and to provide an accurate tool for diagnosis of presymptomatic patients as well as for prenatal diagnosis in the affected families. Methods Polymerase chain reaction/Restriction Fragment Length Polymorphism, were used to detect the four mutations in the AGXT gene in DNA samples from 57 patients belonging to 40 families. Results Two mutations causing PH1 were detected in 24 patients (42.1%), with a predominance of the I244T mutation (68% of patients) and 33_34insC (in the remaining 32%). In 92% of cases, mutated alleles were in homozygous state. The presented clinical features were similar for the two mutations. The age of onset was heterogeneous with a higher frequency of the pediatric age. In 58.3% of cases, the presentation corresponded to advanced renal disease which occurred early (< 5 years) in the two mutations. In adolescents, only the I244T mutation was detected (41.1%). I244T and 33_34insC mutations were observed in adult patients, with 17.6% and 12.5% respectively. Conclusion Limited mutation analysis can provide a useful first line investigation for PH1. I244T and 33_34insC presented 28.2% of identified mutations causing disease in our cohort. This identification could provide an accurate tool for prenatal diagnosis in the affected families, for genetic counselling and for detection of presymptomatic individuals. PMID:21612638

2011-01-01

3

UAS and NextGen  

Microsoft Academic Search

Most UAS currently in use would not meet all the requirements of NextGen. UAS provide a unique opportunity to test many of the technologies and impacts of NextGen. NextGen requirements and capabilities may create a more friendly environment for UAS operations.

B. L. Mulac

2010-01-01

4

GenBank.  

PubMed

The GenBank nucleotide sequence database now contains sequence data and associated annotation corresponding to 56,000,000 nucleotides in 45,000 entries. The input stream of data coming into the database has largely been shifted to direct submissions from the scientific community on electronic media. The data have been installed in a relational database management system and are made available in this form through on-line access, and through various network and off-line computer-readable media. In addition, GenBank provides the U.S. distribution center for the BIOSCI electronic bulletin board service. PMID:2041806

Burks, C; Cassidy, M; Cinkosky, M J; Cumella, K E; Gilna, P; Hayden, J E; Keen, G M; Kelley, T A; Kelly, M; Kristofferson, D

1991-04-25

5

GenBank.  

PubMed

The GenBank nucleotide sequence database now contains sequence data and associated annotation corresponding to 85,000,000 nucleotides in 67,000 entries from a total of 3,000 organisms. The input stream of data coming into the database is primarily as direct submissions from the scientific community on electronic media, with little or no data being keyboarded from the printed page by the databank staff. The data are maintained in a relational database management system and are made available in flatfile form through on-line access, and through various network and off-line computer-readable media. The data are also distributed in relational form through satellite copies at a number of institutions in the U.S. and elsewhere. In addition, GenBank provides the U.S. distribution center for the BIOSCI electronic bulletin board service. PMID:1598235

Burks, C; Cinkosky, M J; Fischer, W M; Gilna, P; Hayden, J E; Keen, G M; Kelly, M; Kristofferson, D; Lawrence, J

1992-05-11

6

tostandoutfromthecrowd? NextGen Immunology  

E-print Network

tostandoutfromthecrowd? Doyouwant NextGen Immunology: The Michael Sela Student and Postdoc Program for Excellence in Immunology Become a leader of NextGen Immunology! The immune system, in addition to its, state-of-the-art immunology is now reemerging as the most rapidly evolving multi-disciplinary biological

Shapiro, Ehud

7

Verifying Test Hypotheses -HOL/TestGen Verifying Test Hypotheses -HOL/TestGen  

E-print Network

Verifying Test Hypotheses - HOL/TestGen Verifying Test Hypotheses - HOL/TestGen An Experiment in Test and Proof Thomas Malcher January 20, 2014 1 / 20 #12;Verifying Test Hypotheses - HOL/TestGen HOL/TestGen Outline Introduction Test Hypotheses HOL/TestGen - Demo Verifying Test Hypotheses Conclusion 2 / 20 #12

8

FutureGen Project Report  

SciTech Connect

This report summarizes the comprehensive siting, permitting, engineering, design, and costing activities completed by the FutureGen Industrial Alliance, the Department of Energy, and associated supporting subcontractors to develop a first of a kind near zero emissions integrated gasification combined cycle power plant and carbon capture and storage project (IGCC-CCS). With the goal to design, build, and reliably operate the first IGCC-CCS facility, FutureGen would have been the lowest emitting pulverized coal power plant in the world, while providing a timely and relevant basis for coal combustion power plants deploying carbon capture in the future. The content of this report summarizes key findings and results of applicable project evaluations; modeling, design, and engineering assessments; cost estimate reports; and schedule and risk mitigation from initiation of the FutureGen project through final flow sheet analyses including capital and operating reports completed under DOE award DE-FE0000587. This project report necessarily builds upon previously completed siting, design, and development work executed under DOE award DE-FC26- 06NT4207 which included the siting process; environmental permitting, compliance, and mitigation under the National Environmental Policy Act; and development of conceptual and design basis documentation for the FutureGen plant. For completeness, the report includes as attachments the siting and design basis documents, as well as the source documentation for the following: • Site evaluation and selection process and environmental characterization • Underground Injection Control (UIC) Permit Application including well design and subsurface modeling • FutureGen IGCC-CCS Design Basis Document • Process evaluations and technology selection via Illinois Clean Coal Review Board Technical Report • Process flow diagrams and heat/material balance for slurry-fed gasifier configuration • Process flow diagrams and heat/material balance for dry-fed gasifier configuration • Full capital cost report and cost category analysis (CAPEX) • Full operating cost report and assumptions (OPEX) Comparative technology evaluations, value engineering exercises, and initial air permitting activities are also provided; the report concludes with schedule, risk, and cost mitigation activities as well as lessons learned such that the products of this report can be used to support future investments in utility scale gasification and carbon capture and sequestration. Collectively, the FutureGen project enabled the comprehensive site specific evaluation and determination of the economic viability of IGCC-CCS. The project report is bound at that determination when DOE formally proposed the FutureGen 2.0 project which focuses on repowering a pulverized coal power plant with oxy-combustion technology including CCS.

Cabe, Jim; Elliott, Mike

2010-09-30

9

Introduction to GenCade Ashley Frey  

E-print Network

Bay Ebb shoal Dune erosion Wind-blown sand Overwash Atlantic Ocean Coastal Structures: · Impoundment, Coastal Inlets Research Program, 16-18 October 2012 2 Outline · What is GenCade? · Background, overviewCade Webinar, Coastal Inlets Research Program, 16-18 October 2012 3 GENESIS + Cascade GenCade Cascade (top

US Army Corps of Engineers

10

DefinitionCode Gen Ed Code Definitions  

E-print Network

CLASSICS 224 Greek Mythology AL CLASSICS 261 Greek Voices AL CLASSICS 263 Classical Echoes AL CLASSICS 365 Classical Greek Prose AL ITALIAN 514 The Early Renaissance AL JAPANESE 144 Japan Lit-Modern AL JUDAIC 319 Scandinavian Mythology 1 3/25/2014 #12;Catalog # Gen Ed Class Title Gen Ed Classes: Fall 2014 DESCR.A AL

Massachusetts at Amherst, University of

11

Proposal of the genera Anaerococcus gen. nov., Peptoniphilus gen. nov. and Gallicola gen. nov. for members of the genus Peptostreptococcus.  

PubMed

Members of genus Peptostreptococcus have previously been found to be distantly related to the type species, Peptostreptococcus anaerobius, on the basis of 16S rDNA sequence similarities. They were divided into three major phylogenetic groups, and their peptidoglycan structure and biochemical traits differed between groups. The reclassification of the species of these three groups into three new genera, Peptoniphilus gen. nov., Anaerococcus gen. nov. and Gallicola gen. nov., is proposed. The genus Peptoniphilus gen. nov. includes the following butyrate-producing, non-saccharolytic species that use peptone and amino acids as major energy sources: Peptoniphilus asaccharolyticus comb. nov. (type species), Peptoniphilus lacrimaris comb. nov., Peptoniphilus harei comb. nov., Peptoniphilus indolicus comb. nov. and Peptoniphilus ivorii comb. nov. The genus Anaerococcus gen. nov. contains the saccharolytic, butyrate-producing species Anaerococcus prevotii comb. nov. (type species), Anaerococcus tetradius comb. nov., Anaerococcus lactolyticus comb. nov., Anaerococcus hydrogenalis comb. nov., Anaerococcus vaginalis comb. nov. and Anaerococcus octavius sp. nov. The genus Gallicola gen. nov. contains a single species, Gallicola barnesae comb. nov. PMID:11491354

Ezaki, T; Kawamura, Y; Li, N; Li, Z Y; Zhao, L; Shu, S

2001-07-01

12

AutoGen Version 5.0  

NASA Technical Reports Server (NTRS)

Version 5.0 of the AutoGen software has been released. Previous versions, variously denoted Autogen and autogen, were reported in two articles: Automated Sequence Generation Process and Software (NPO-30746), Software Tech Briefs (Special Supplement to NASA Tech Briefs), September 2007, page 30, and Autogen Version 2.0 (NPO- 41501), NASA Tech Briefs, Vol. 31, No. 10 (October 2007), page 58. To recapitulate: AutoGen (now signifying automatic sequence generation ) automates the generation of sequences of commands in a standard format for uplink to spacecraft. AutoGen requires fewer workers than are needed for older manual sequence-generation processes, and greatly reduces sequence-generation times. The sequences are embodied in spacecraft activity sequence files (SASFs). AutoGen automates generation of SASFs by use of another previously reported program called APGEN. AutoGen encodes knowledge of different mission phases and of how the resultant commands must differ among the phases. AutoGen also provides means for customizing sequences through use of configuration files. The approach followed in developing AutoGen has involved encoding the behaviors of a system into a model and encoding algorithms for context-sensitive customizations of the modeled behaviors. This version of AutoGen addressed the MRO (Mars Reconnaissance Orbiter) primary science phase (PSP) mission phase. On previous Mars missions this phase has more commonly been referred to as mapping phase. This version addressed the unique aspects of sequencing orbital operations and specifically the mission specific adaptation of orbital operations for MRO. This version also includes capabilities for MRO s role in Mars relay support for UHF relay communications with the MER rovers and the Phoenix lander.

Gladden, Roy E.; Khanampornpan, Teerapat; Fisher, Forest W.

2010-01-01

13

Unleashing Gen Y: Marketing Mars to Millennials  

NASA Technical Reports Server (NTRS)

Space advocates need to engage Generation Y (born 1977-1999).This outreach is necessary to recruit the next generation of scientists and engineers to explore Mars. Space advocates in the non-profit, private, and government sectors need to use a combination of technical communication, marketing, and politics, to develop messages that resonate with Gen Y. Until now, space messages have been generated by and for college-educated white males; Gen Y is much more diverse, including as much as one third minorities. Young women, too, need to be reached. My research has shown that messages emphasizing technology, fun, humor, and opportunity are the best means of reaching the Gen Y audience of 60 million (US population is 300 million). The important things space advocates must avoid are talking down to this generation, making false promises, or expecting them to "wait their turn" before they can participate. This is the MTV generation! We need to find ways of engaging Gen Y now to build a future where human beings can live and work on the planet Mars. In addition to the messages themselves, advocates need to keep up with Gen Y' s social networking and use of iPods, cell phones, and the Internet. NASA and space advocacy groups can use these tools for "viral marketing," where young people share targeted space-related information via cell phones or the Internet because they like it. Overall, Gen Y is a socially dynamic and media-savvy group; advocates' space messages need to be sincere, creative, and placed in locations where Gen Y lives. Mars messages must be memorable!

Leahy, Bart D.; Hidalgo, Loretta; Kloberdanz, Cassie

2007-01-01

14

LINK2009 FASE 1 UDVIKLING AF 2. GEN. BRNDSELSCELLE  

E-print Network

EUDP programmet til udvikling og demon- stration af 2. gen. brint og brændselscelle teknologi til- land projekt" (ENS-33032-0208) hvor 1. Gen. teknologi blev udviklet og afprøvet. Specifikt var målet i to faser, med fase 1 indeholdende udviklingen af 2. Gen. teknologi, og en senere fase 2 indeholdende de

15

GenEng: A dialogue-based natural language interface to the GenBank  

SciTech Connect

To sequence all the genes in human DNA and analyze their functions, the Human Genome Project has been collecting a large body of data in data banks such as GenBank{copyright}. One of the important issues concerning computational biologists is the availability of the tools which can provide easy and efficient access to these data banks. In this paper, the author will give a brief overview of different approaches to the design of a relational database interface. The paper concentrates on the design of GenEng, a dialogue based natural language interface for information retrieval from the GenBank relational database.

Karimi, E. [Univ. of Texas System, Austin, TX (United States)

1993-12-31

16

Crane Scheduling for ABB: Progress Latife Gen  

E-print Network

1 Crane Scheduling for ABB: Progress Report Ionu Aron Latife Genç John Hooker March 2006 #12;2 Problem · Schedule 2 cranes to transfer material between locations in a copper processing facility. ­ Some require several stops. ­ Cranes run on the same track. · Objective: minimize total penalty ­ Penalties

Grossmann, Ignacio E.

17

Gen IV Materials Handbook Implementation Plan  

SciTech Connect

A Gen IV Materials Handbook is being developed to provide an authoritative single source of highly qualified structural materials information and materials properties data for use in design and analyses of all Generation IV Reactor Systems. The Handbook will be responsive to the needs expressed by all of the principal government, national laboratory, and private company stakeholders of Gen IV Reactor Systems. The Gen IV Materials Handbook Implementation Plan provided here addresses the purpose, rationale, attributes, and benefits of the Handbook and will detail its content, format, quality assurance, applicability, and access. Structural materials, both metallic and ceramic, for all Gen IV reactor types currently supported by the Department of Energy (DOE) will be included in the Gen IV Materials Handbook. However, initial emphasis will be on materials for the Very High Temperature Reactor (VHTR). Descriptive information (e.g., chemical composition and applicable technical specifications and codes) will be provided for each material along with an extensive presentation of mechanical and physical property data including consideration of temperature, irradiation, environment, etc. effects on properties. Access to the Gen IV Materials Handbook will be internet-based with appropriate levels of control. Information and data in the Handbook will be configured to allow search by material classes, specific materials, specific information or property class, specific property, data parameters, and individual data points identified with materials parameters, test conditions, and data source. Details on all of these as well as proposed applicability and consideration of data quality classes are provided in the Implementation Plan. Website development for the Handbook is divided into six phases including (1) detailed product analysis and specification, (2) simulation and design, (3) implementation and testing, (4) product release, (5) project/product evaluation, and (6) product maintenance and enhancement. Contracting of development of the Handbook website is discussed in terms of host server options, cost, technology, developer background and cooperative nature, and company stability. One of the first and most important activities in website development will be the generation of a detailed Handbook product requirements document including case diagrams and functional requirements tables. The Implementation Plan provides a detailed overview of the organizational structure of the Handbook and details of Handbook preparation, publication, and distribution. Finally, the Implementation Plan defines Quality Assurance requirements for the Handbook.

Rittenhouse, P.; Ren, W.

2005-03-29

18

Complications Following BellaGen(TM) Injection  

PubMed Central

BellaGen™ is an injectable acellular dermal matrix granule derived from donated human skin tissue that was recently developed for soft tissue augmentation. Its use has been sporadically reported in penile girth enhancement procedures. Many cases of complications have been reported after injecting acellular dermal matrices like AlloDerm or SureDerm™ but few reports on complications associated with BellaGen™ injection. We report here on penile skin inflammation and necrosis following augmentation phalloplasty with BellaGen™, which developed 3 days after the injection and persisted for more than 2 weeks. The patient had a 15 year history of type 2 diabetes mellitus, and he was treated with oral antibiotics and wet dressings with KMNO4 solution to combine preservation of the remaining penile soft tissue with debridement of avascular tissue. The lesion improved with this treatment, but the patient experienced pain for about 2 weeks. All patients should be informed of the potential complications with the use of injectable acellular dermal matrices before treatment. Patient selection for augmentation is also important to have the most desirable results. PMID:22346264

Park, Mi Kyung; Kim, Hyun Kyu; Park, Kui Young; Li, Kapsok; Hong, Chang Kwun

2011-01-01

19

Complications Following BellaGen™ Injection.  

PubMed

BellaGen™ is an injectable acellular dermal matrix granule derived from donated human skin tissue that was recently developed for soft tissue augmentation. Its use has been sporadically reported in penile girth enhancement procedures. Many cases of complications have been reported after injecting acellular dermal matrices like AlloDerm or SureDerm™ but few reports on complications associated with BellaGen™ injection. We report here on penile skin inflammation and necrosis following augmentation phalloplasty with BellaGen™, which developed 3 days after the injection and persisted for more than 2 weeks. The patient had a 15 year history of type 2 diabetes mellitus, and he was treated with oral antibiotics and wet dressings with KMNO4 solution to combine preservation of the remaining penile soft tissue with debridement of avascular tissue. The lesion improved with this treatment, but the patient experienced pain for about 2 weeks. All patients should be informed of the potential complications with the use of injectable acellular dermal matrices before treatment. Patient selection for augmentation is also important to have the most desirable results. PMID:22346264

Park, Mi Kyung; Kim, Hyun Kyu; Park, Kui Young; Li, Kapsok; Seo, Seong Jun; Hong, Chang Kwun

2011-12-01

20

Composition Validation and Subjectivity in GenVoca Generators  

Microsoft Academic Search

GenVoca generators synthesize software systems by composing components from reuse libraries. GenVoca components are designed to export and import standardized interfaces, and thus be plug- compatible, interchangeable, and interoperable with other components. In this paper, we examine two different but important issues in software system synthesis. First, not all syntactically correct compositions of components are semantically correct. We present simple,

Don S. Batory; Bart J. Geraci

1997-01-01

21

TidGen Power System Commercialization Project  

SciTech Connect

ORPC Maine, LLC, a wholly-owned subsidiary of Ocean Renewable Power Company, LLC (collectively ORPC), submits this Final Technical Report for the TidGen® Power System Commercialization Project (Project), partially funded by the U.S. Department of Energy (DE-EE0003647). The Project was built and operated in compliance with the Federal Energy Regulatory Commission (FERC) pilot project license (P-12711) and other permits and approvals needed for the Project. This report documents the methodologies, activities and results of the various phases of the Project, including design, engineering, procurement, assembly, installation, operation, licensing, environmental monitoring, retrieval, maintenance and repair. The Project represents a significant achievement for the renewable energy portfolio of the U.S. in general, and for the U.S. marine hydrokinetic (MHK) industry in particular. The stated Project goal was to advance, demonstrate and accelerate deployment and commercialization of ORPC’s tidal-current based hydrokinetic power generation system, including the energy extraction and conversion technology, associated power electronics, and interconnection equipment capable of reliably delivering electricity to the domestic power grid. ORPC achieved this goal by designing, building and operating the TidGen® Power System in 2012 and becoming the first federally licensed hydrokinetic tidal energy project to deliver electricity to a power grid under a power purchase agreement in North America. Located in Cobscook Bay between Eastport and Lubec, Maine, the TidGen® Power System was connected to the Bangor Hydro Electric utility grid at an on-shore station in North Lubec on September 13, 2012. ORPC obtained a FERC pilot project license for the Project on February 12, 2012 and the first Maine Department of Environmental Protection General Permit issued for a tidal energy project on January 31, 2012. In addition, ORPC entered into a 20-year agreement with Bangor Hydro Electric Company on January 1, 2013 for up to 5 megawatts at a price of $215/MWh, escalating at 2.0% per year.

Sauer, Christopher R. [President & CEO] [President & CEO; McEntee, Jarlath [VP Engineering & CTO] [VP Engineering & CTO

2013-12-30

22

Back to the FutureGen?  

SciTech Connect

After years of political wrangling, Democrats may green-light the experimental clean coal power plants. The article relates how the project came to be curtailed, how Senator Dick Durbin managed to protect $134 million in funding for FutureGen in Mattoon, and how once Obama was in office a $2 billion line item to fund a 'near zero emissions power plant(s)' was placed in the Senate version of the Stimulus Bill. The final version of the legislation cut the funding to $1 billion for 'fossil energy research and development'. In December 2008 the FutureGen Alliance and the City of Mattoon spent $6.5 billion to purchase the plants eventual 440 acre site. A report by the Government Accountability Office (GAO) said that Bush's inaction may have set back clean coal technology in the US by as much as a decade. If additional funding comes through construction of the plant could start in 2010. 1 fig., 1 photo.

Buchsbaum, L.

2009-04-15

23

Head-Worn Displays for NextGen  

NASA Technical Reports Server (NTRS)

The operating concepts emerging under the Next Generation air transportation system (NextGen) require new technology and procedures - not only on the ground-side - but also on the flight deck. Flight deck display and decision support technologies are specifically targeted to overcome aircraft safety barriers that might otherwise constrain the full realization of NextGen. One such technology is the very lightweight, unobtrusive head-worn display (HWD). HWDs with an integrated head-tracking system are being researched as they offer significant potential benefit under emerging NextGen operational concepts. Two areas of benefit for NextGen are defined. First, the HWD may be designed to be equivalent to the Head-Up Display (HUD) using Virtual HUD concepts. As such, these operational credits may be provided to significantly more aircraft for which HUD installation is neither practical nor possible. Second, the HWD provides unique display capabilities, such as an unlimited field-of-regard. These capabilities may be integral to emerging NextGen operational concepts, eliminating safety issues which might otherwise constrain the full realization of NextGen. The paper details recent research results, current HWD technology limitations, and future technology development needed to realize HWDs as a enabling technology for NextGen.

Bailey, Randall E.; Shelton, Kevin J.; Arthur, J. J.

2011-01-01

24

Proposal for two new genera, Brevibacillus gen. nov. and Aneurinibacillus gen. nov.  

PubMed

16S rRNA gene sequences of the type strains of 11 species belonging to the Bacillus brevis and Bacillus aneurinolyticus groups were determined. On the basis of the results of gene sequence analyses, these species were separated into two clusters. The B. brevis cluster included 10 species, namely, Bacillus brevis, Bacillus agri, Bacillus centrosporus, Bacillus choshinensis, Bacillus parabrevis, Bacillus reuszeri, Bacillus formosus, Bacillus borstelensis, Bacillus laterosporus, and Bacillus thermoruber. Bacillus aneurinolyticus and Bacillus migulanus belonged to the B. aneurinolyticus cluster. Moreover, the two clusters were phylogenetically distinct from other Bacillus, Amphibacillus, Sporolactobacillus, Paenibacillus, and Alicyclobacillus species. On the basis of our data, we propose reclassification of the B. brevis cluster as Brevibacillus gen. nov. and reclassification of the B. aneurinolyticus cluster as Aneurinibacillus gen. nov. By using 16S rRNA gene sequence alignments, two specific PCR amplification primers were designed for differentiating the two new genera from each other and from other aerobic, endospore-forming organisms. PMID:8863420

Shida, O; Takagi, H; Kadowaki, K; Komagata, K

1996-10-01

25

NextGen Future Safety Assessment Game  

NASA Technical Reports Server (NTRS)

The successful implementation of the next generation infrastructure systems requires solid understanding of their technical, social, political and economic aspects along with their interactions. The lack of historical data that relate to the long-term planning of complex systems introduces unique challenges for decision makers and involved stakeholders which in turn result in unsustainable systems. Also, the need to understand the infrastructure at the societal level and capture the interaction between multiple stakeholders becomes important. This paper proposes a methodology in order to develop a holistic approach aiming to provide an alternative subject-matter expert (SME) elicitation and data collection method for future sociotechnical systems. The methodology is adapted to Next Generation Air Transportation System (NextGen) decision making environment in order to demonstrate the benefits of this holistic approach.

Ancel, Ersin; Gheorghe, Adian; Jones, Sharon Monica

2010-01-01

26

EPCGen2 pseudorandom number generators: analysis of J3Gen.  

PubMed

This paper analyzes the cryptographic security of J3Gen, a promising pseudo random number generator for low-cost passive Radio Frequency Identification (RFID) tags. Although J3Gen has been shown to fulfill the randomness criteria set by the EPCglobal Gen2 standard and is intended for security applications, we describe here two cryptanalytic attacks that question its security claims: (i) a probabilistic attack based on solving linear equation systems; and (ii) a deterministic attack based on the decimation of the output sequence. Numerical results, supported by simulations, show that for the specific recommended values of the configurable parameters, a low number of intercepted output bits are enough to break J3Gen. We then make some recommendations that address these issues. PMID:24721767

Peinado, Alberto; Munilla, Jorge; Fúster-Sabater, Amparo

2014-01-01

27

1. GENERAL VIEW. Statues: Maj. Gen George Meade by Daniel ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

1. GENERAL VIEW. Statues: Maj. Gen George Meade by Daniel Chester French, south side; Maj. Gen. John Reynolds by Charles Grafly, north side. Equestrian Statues: Maj. Gen George B. McClellan by Edward C. Potter, south side; Maj. Gen Winfield S. Hancock by J.Q.A. Ward, north side. The statue at the base of northern inner pedestal is Richard Smith, a type founder and donor of the Memorial. The niches are filled with eight colossal busts including Union generals, admirals, Pennsylvania governor, Memorial's architects (John T. and James H. Windrim), and executor of Smith's will. The frieze is carved with the names of eighty-four prominent Pennsylvania participants in the Civil War. - Smith Memorial Arch, Philadelphia, Philadelphia County, PA

28

College of Agriculture, Food and Environment GEN General Agriculture  

E-print Network

College of Agriculture, Food and Environment GEN General Agriculture KEY: # = new course * = course IN AGRICULTURE. (3) Anintroductorycourserequiringcriticalanalysisofthemajorsocial. Prereq: Students enrolled in the College of Agriculture; freshmen only in fall semesters and transfers

MacAdam, Keith

29

Combivena gen.n (Hymenoptera: Ichneumonidae: Acaenitinae) from China.  

PubMed

Combivena Sheng & Sun, gen.n. and Combivena sulcata Sheng & Sun, sp.n. belonging to Acaenitinae of family Ichneumonidae (Hymenoptera), collected from Qinghai Province, China, are described and illustrated. PMID:25347843

Sheng, Mao-Ling; Sun, Shu-Ping

2014-01-01

30

FutureGen Project Report, Final Technical Report.  

National Technical Information Service (NTIS)

This report summarizes the comprehensive siting, permitting, engineering, design, and costing activities completed by the FutureGen Industrial Alliance, the Department of Energy, and associated supporting subcontractors to develop a first of a kind near z...

J. Cabe, M. Elliott

2010-01-01

31

ModGen: a model generator for instrumentation analysis  

Microsoft Academic Search

A computer software tool for the automatic generation of steady-state process models to be used in instrumentation analysis was developed. We describe the program, called ModGen, discussing its main advantages and potential benefits. ModGen constitutes the front-end of a complete decision support system (DSS) for plant instrumentation design and revamp. This DSS is currently under development. The paper concludes with

G. E. Vazquez; I. Ponzoni; M. C. Sánchez; N. B. Brignole

2001-01-01

32

A Novel Role of Human Holliday Junction Resolvase GEN1 in the Maintenance of Centrosome Integrity  

PubMed Central

The maintenance of genomic stability requires accurate genome replication, repair of DNA damage, and the precise segregation of chromosomes in mitosis. GEN1 possesses Holliday junction resolvase activity in vitro and presumably functions in homology driven repair of DNA double strand breaks. However, little is currently known about the cellular functions of human GEN1. In the present study we demonstrate that GEN1 is a novel centrosome associated protein and we characterize the various phenotypes associated with GEN1 deficiency. We identify an N-terminal centrosome localization signal in GEN1, which is required and sufficient for centrosome localization. We report that GEN1 depletion results in aberrant centrosome numbers associated with the formation of multiple spindle poles in mitosis, an increased number of cells with multi-nuclei, increased apoptosis and an elevated level of spontaneous DNA damage. We find homologous recombination severely impaired in GEN1 deficient cells, suggesting that GEN1 functions as a Holliday junction resolvase in vivo as well as in vitro. Complementation of GEN1 depleted cells with various GEN1 constructs revealed that centrosome association but not catalytic activity of GEN1 is required for preventing centrosome hyper-amplification, formation of multiple mitotic spindles, and multi-nucleation. Our findings provide novel insight into the biological functions of GEN1 by uncovering an important role of GEN1 in the regulation of centrosome integrity. PMID:23166748

Zhou, Dong-Ping; Xu, Qian; Li, Miao-Miao; Wang, Zhao-Qi; Tong, Wei-Min; Yang, Yun-Gui

2012-01-01

33

Parachloroidium gen. nov. (Trebouxiophyceae, Chlorophyta), a novel genus of coccoid green algae from subaerial corticolous biofilms  

E-print Network

Parachloroidium gen. nov. (Trebouxiophyceae, Chlorophyta), a novel genus of coccoid green algae. Parachloroidium gen. nov. (Trebouxiophyceae, Chlorophyta), a novel genus of coccoid green algae from subaerial the Parachloroidium strains from other similar green algae. However, ultrastructural characteristics and molecular

34

HydroGen: Automatically Generating Self-Assembly Code for Hydron Units  

E-print Network

HydroGen: Automatically Generating Self-Assembly Code for Hydron Units George Konidaris, Tim Taylor, jhallamg@inf.ed.ac.uk Abstract. This paper introduces HydroGen, an object compiler system that produces, and are thus free of the constraints of gravity. This system, called HydroGen, is therefore able to assemble

Massachusetts at Amherst, University of

35

Training trust in automation within a NextGen environment  

NASA Astrophysics Data System (ADS)

The projected increase in air traffic density has led to the development of NextGen that is expected to revolutionize the way the NAS is currently functioning. For NextGen to be implemented successfully, it is important to understand the humanautomation relationship within a complex system. Controllers will have to rely on automated tools to successfully manage aircraft in their sector. Increasing human trust in automation can lead to an increase in automation acceptance and its proper use. However, we are not aware of any research studies that have attempted to directly train individuals to trust automation. We report on an attempt to train 8 novice air traffic controllers to trust the automated NextGen tools in a radar internship course. Although the results were not statistically significant, the trend in the data suggests that it may be possible to train trust in automation.

Higham, Tiana-Lynn M.

36

Enhancing phylogeography by improving geographical information from GenBank.  

PubMed

Phylogeography is a field that focuses on the geographical lineages of species such as vertebrates or viruses. Here, geographical data, such as location of a species or viral host is as important as the sequence information extracted from the species. Together, this information can help illustrate the migration of the species over time within a geographical area, the impact of geography over the evolutionary history, or the expected population of the species within the area. Molecular sequence data from NCBI, specifically GenBank, provide an abundance of available sequence data for phylogeography. However, geographical data is inconsistently represented and sparse across GenBank entries. This can impede analysis and in situations where the geographical information is inferred, and potentially lead to erroneous results. In this paper, we describe the current state of geographical data in GenBank, and illustrate how automated processing techniques such as named entity recognition, can enhance the geographical data available for phylogeographic studies. PMID:21723960

Scotch, Matthew; Sarkar, Indra Neil; Mei, Changjiang; Leaman, Robert; Cheung, Kei-Hoi; Ortiz, Pierina; Singraur, Ashutosh; Gonzalez, Graciela

2011-12-01

37

Platelike structures of semiconductor clusters Gen (n=40-44)  

NASA Astrophysics Data System (ADS)

The structures of Gen (n =40-44) clusters were searched by genetic algorithm combined with a tight-binding method. First-principles calculations based on density functional theory were performed to further optimize the isomer structures. The calculated results show that Gen (n =40-44) clusters favor platelike structures, consisted of four small magic clusters (Ge9 or Ge10), and a Ge4 core. The Ge4 core along with the parts of the four linked small clusters forms a diamond segment. The cluster mobilities of the most stable structures are in good agreement with the experimental data.

Qin, Wei; Lu, Wen-Cai; Zhao, Li-Zhen; Zang, Qing-Jun; Chen, Guang-Ju; Wang, C. Z.; Ho, K. M.

2009-09-01

38

Geometric structures of Gen (n=34-39) clusters  

NASA Astrophysics Data System (ADS)

The structures of Gen (n=34-39) clusters were searched by a genetic algorithm using a tight-binding interatomic potential. First-principles calculations based on density functional theory were performed to further identify the lowest-energy structures. The calculated results show that Gen (n=34-39) clusters favor prolate or Y-shaped three-arm structures consisting of two or three small stable clusters (Ge6, Ge7, Ge9, or Ge10) linked by a Ge6 or Ge9 bulk unit. The calculated results suggest the transition point from prolate to Y-shaped three-arm structures appears at Ge35 or Ge36.

Qin, Wei; Lu, Wen-Cai; Zang, Qing-Jun; Zhao, Li-Zhen; Chen, Guang-Ju; Wang, C. Z.; Ho, K. M.

2010-06-01

39

76 FR 28973 - Terra-Gen Dixie Valley, LLC; Order on Rehearing and Accepting Tariff Filing, Subject to...  

Federal Register 2010, 2011, 2012, 2013

...Terra-Gen's future use of the Dixie Valley Line. Contrary to the situation...Terra-Gen's existing use of the Dixie Valley Line, Terra-Gen is not currently...Terra-Gen will provide on the Dixie Valley Line.\\14\\ We find that...P 109. \\19\\ See Entergy Mississippi, Inc., 112 FERC ]...

2011-05-19

40

Welcome to the 1st GenCade Ashley Frey  

E-print Network

Welcome to the 1st GenCade Webinar Ashley Frey Research Civil Engineer, Co-PI of the InletCade Webinar, Coastal Inlets Research Program, 16-18 October Webinar will be presentation and demonstration staff will assist with answering questions during the webinar. � Instructor may use extra time (if any

US Army Corps of Engineers

41

Competitive Learning for Deep Temporal Networks Robert Gens  

E-print Network

Competitive Learning for Deep Temporal Networks Robert Gens Computer Science and Engineering of competitive learning in deep networks for understanding sequential data. Hierarchies of competitive learning algorithms have been found in the brain [1] and their use in deep vision networks has been validated [2

Anderson, Richard

42

ANNEXES -69 -4.4 Annexe GEN & DU  

E-print Network

((null x) t) ((test (car x)) (list-test (cdr x))) )) (defun bod (x) (or (terme x) (prop x) (exp-cond x (print (read-char)) ! (go b)) ) (defun gen (x) (prog (a) (setq a x) b (setq a (next-a a)) (cond ((bod

Marchal, Bruno

43

An electronic flight bag for NextGen avionics  

NASA Astrophysics Data System (ADS)

The introduction of the Next Generation Air Transportation System (NextGen) initiative by the Federal Aviation Administration (FAA) will impose new requirements for cockpit avionics. A similar program is also taking place in Europe by the European Organisation for the Safety of Air Navigation (Eurocontrol) called the Single European Sky Air Traffic Management Research (SESAR) initiative. NextGen will require aircraft to utilize Automatic Dependent Surveillance-Broadcast (ADS-B) in/out technology, requiring substantial changes to existing cockpit display systems. There are two ways that aircraft operators can upgrade their aircraft in order to utilize ADS-B technology. The first is to replace existing primary flight displays with new displays that are ADS-B compatible. The second, less costly approach is to install an advanced Class 3 Electronic Flight Bag (EFB) system. The installation of Class 3 EFBs in the cockpit will allow aircraft operators to utilize ADS-B technology in a lesser amount of time with a decreased cost of implementation and will provide additional benefits to the operator. This paper describes a Class 3 EFB, the NexisTM Flight-Intelligence System, which has been designed to allow users a direct interface with NextGen avionics sensors while additionally providing the pilot with all the necessary information to meet NextGen requirements.

Zelazo, D. Eyton

2012-06-01

44

EnGenIUS -- Environmental Genome Informational Utility System.  

PubMed

Short-insert shotgun sequencing approaches have been applied in recent years to environmental genomic libraries. In the case of complex multispecies microbial communities, there can be many sequence reads that are not incorporated into assemblies, and thus need to be annotated and accessible as single reads. Most existing annotation systems and genome databases accommodate assembled genomes containing contiguous gene-encoding sequences. Thus, a solution is required that can work effectively with environmental genomic annotation information to facilitate data analysis. The Environmental Genome Informational Utility System (EnGenIUS) is a comprehensive environmental genome (metagenome) research toolset that was specifically designed to accommodate the needs of large (> 250 K sequence reads) environmental genome sequencing efforts. The core EnGenIUS modules consist of a set of UNIX scripts and PHP programs used for data preprocessing, an annotation pipeline with accompanying analysis tools, two entity relational databases, and a graphical user interface. The annotation pipeline has a modular structure and can be customized to best fit input data set properties. The integrated entity relational databases store raw data and annotation analysis results. Access to the underlying databases and services is facilitated through a web-based graphical user interface. Users have the ability to browse, upload, download, and analyze preprocessed data, based on diverse search criteria. The EnGenIUS toolset was successfully tested using the Alvinella pompejana epibiont environmental genome data set, which comprises more than 300 K sequence reads. A fully browsable EnGenIUS portal is available at (http://ocean.dbi.udel.edu/) (access code: "guest"). The scope of this paper covers the implementation details and technical aspects of the EnGenIUS toolset. PMID:19090024

Kaplarevic, Mihailo; Murray, Alison E; Cary, Stephen C; Gao, Guang R

2008-12-01

45

J3Gen: a PRNG for low-cost passive RFID.  

PubMed

Pseudorandom number generation (PRNG) is the main security tool in low-cost passive radio-frequency identification (RFID) technologies, such as EPC Gen2. We present a lightweight PRNG design for low-cost passive RFID tags, named J3Gen. J3Gen is based on a linear feedback shift register (LFSR) configured with multiple feedback polynomials. The polynomials are alternated during the generation of sequences via a physical source of randomness. J3Gen successfully handles the inherent linearity of LFSR based PRNGs and satisfies the statistical requirements imposed by the EPC Gen2 standard. A hardware implementation of J3Gen is presented and evaluated with regard to different design parameters, defining the key-equivalence security and nonlinearity of the design. The results of a SPICE simulation confirm the power-consumption suitability of the proposal. PMID:23519344

Melià-Seguí, Joan; Garcia-Alfaro, Joaquin; Herrera-Joancomartí, Jordi

2013-01-01

46

Advanced Vehicle Concepts and Implications for NextGen  

NASA Technical Reports Server (NTRS)

This report presents the results of a major NASA study of advanced vehicle concepts and their implications for the Next Generation Air Transportation System (NextGen). Comprising the efforts of dozens of researchers at multiple institutions, the analyses presented here cover a broad range of topics including business-case development, vehicle design, avionics, procedure design, delay, safety, environmental impacts, and metrics. The study focuses on the following five new vehicle types: Cruise-efficient short takeoff and landing (CESTOL) vehicles Large commercial tiltrotor aircraft (LCTRs) Unmanned aircraft systems (UAS) Very light jets (VLJs) Supersonic transports (SST). The timeframe of the study spans the years 2025-2040, although some analyses are also presented for a 3X scenario that has roughly three times the number of flights as today. Full implementation of NextGen is assumed.

Blake, Matt; Smith, Jim; Wright, Ken; Mediavilla Ricky; Kirby, Michelle; Pfaender, Holger; Clarke, John-Paul; Volovoi, Vitali; Dorbian, Christopher; Ashok, Akshay; Reynolds, Tom; Waitz, Ian; Hileman, James; Arunachalam, Sarav; Hedrick, Matt; Vempati, Lakshmi; Laroza, Ryan; denBraven, Wim; Henderson, Jeff

2010-01-01

47

ROMS , GENS DU VOYAGE ET EXCLUS SOCIAUX . LES DESTINEES CATEGORIELLES DES TSIGANES NOMADES AU  

E-print Network

», « GENS DU VOYAGE » ET « EXCLUS SOCIAUX ». LES DESTINEES CATEGORIELLES DES « TSIGANES NOMADES » AU COURS-80-86311-24-1 ------------------------------------------------------------------------------------- Pour citer cet article : Mathieu Plésiat, « `Roms', `Gens du voyage' et `exclus sociaux'. Les destinées-88. ------------------------------------------------------------------------------------- #12;71 « Roms », « Gens du voyage » et « exclus sociaux » : les destinées catégorielles des « Tsiganes

Boyer, Edmond

48

PROCESSING OF SPENT TRISO-COATED GEN IV REACTOR FUELS  

Microsoft Academic Search

The crush-leach process was investigated as a method to treat GEN IV TRISO-coated reactor fuels. The method retains the bulk of the carbon components in elemental form, which is favorable for achieving waste reduction goals. A literature review identified the potential problems with this technique. Leaching of simulated crushed TRISO-coated fuel and extraction behavior of the separated leaching solution were

B. B. Spencer; C. H. Mattus; G. D. Del Cul; R. D. Hunt; E. D. Collins

49

NextGen flight security risk assessment information concept  

Microsoft Academic Search

One of the foundational elements of the Next Generation Air Transportation System (NextGen) Secure Airspace concept is the flight security risk assessment. This risk assessment is continually performed and updated based on changes to security-related information pertaining to a particular flight, as well as changes to the security environment external to the flight; e.g., other flights, airports, and airspace. This

C. N. Bolczak; V. Fong; R. Jehlen

2009-01-01

50

GEN IV reactors: Where we are, where we should go  

SciTech Connect

GEN IV power plants represent the mid-long term option of the nuclear sector. International literature proposes many papers and reports dealing with these reactors, but there is an evident difference of type and shape of information making impossible each kind of detailed comparison. Moreover, authors are often strongly involved in some particular design; this creates many difficulties in their super-partes position. Therefore it is necessary to put order in the most relevant information to understand strengths and weaknesses of each design and derive an overview useful for technicians and policy makers. This paper presents the state-of the art for GEN IV nuclear reactors providing a comprehensive literature review of the different designs with a relate taxonomy. It presents the more relevant references, data, advantages, disadvantages and barriers to the adoptions. In order to promote an efficient and wide adoption of GEN IV reactors the paper provides the pre-conditions that must be accomplished, enabling factors promoting the implementation and barriers limiting the extent and intensity of its implementation. It concludes outlying the state of the art of the most important R and D areas and the future achievements that must be accomplished for a wide adoption of these technologies. (authors)

Locatelli, G. [Univ. of Lincoln, Lincoln School of Engineering, Brayford Pool - Lincoln LN6 7TS (United Kingdom); Mancini, M.; Todeschini, N. [Politecnico di Milano, Dept. of Management, Economics and Industrial Engineering, Via Lambruschini 4/B, Milano (Italy)

2012-07-01

51

FutureGen: Pathway to Near-Zero Emissions and Sustainable Energy.  

National Technical Information Service (NTIS)

This presentation will highlight the U.S. Department of Energys (DOE) FutureGen project - a $1 billion government-industry partnership to design, build, and operate a near-zero emissions coal-fueled power plant. The lead organization for the FutureGen ini...

S. E. Zitney, T. A. Sarkus

2007-01-01

52

Pseudorhombodinium lisbonense gen. et sp. nov., a new dinoflagellate fossil from the Lisbon formation (middle Eocene), Little Stave Creek, Alabama  

Microsoft Academic Search

Specimens of Pseudorhombodinium lisbonense gen. et sp. nov., the type species of the new fossil dinoflagellate genus Pseudorhombodinium gen. nov., were recovered from an outcrop of the lower part of the Lisbon Formation (middle Eocene) in Little Stave Creek, Clarke County, Alabama. The sample containing P. lisbonense gen. et sp. nov. is a calcareous glauconitic sand bed located approximately 104

John H. Wrenn

1996-01-01

53

Spatial control of the GEN1 Holliday junction resolvase ensures genome stability  

PubMed Central

Holliday junction (HJ) resolvases are necessary for the processing of persistent recombination intermediates before cell division. Their actions, however, need to be restricted to the late stages of the cell cycle to avoid the inappropriate cleavage of replication intermediates. Control of the yeast HJ resolvase, Yen1, involves phosphorylation changes that modulate its catalytic activity and nuclear import. Here, we show that GEN1, the human ortholog of Yen1, is regulated by a different mechanism that is independent of phosphorylation. GEN1 is controlled exclusively by nuclear exclusion, driven by a nuclear export signal (NES) that restricts GEN1 actions to mitosis when the nuclear membrane breaks down. Construction of a nuclear-localized version of GEN1 revealed that its premature actions partially suppress phenotypes associated with loss of BLM and MUS81, but cause elevated crossover formation. The spatial control of GEN1 therefore contributes to genome stability, by avoiding competition with non-crossover promoting repair pathways. PMID:25209024

Chan, Ying Wai; West, Stephen C.

2014-01-01

54

TelDB: GenLink Multimedia Telomere Resource  

NSDL National Science Digital Library

This TelDB metasite provides information on telomere research and a searchable citations database, including over 1100 telomere-related citations from 200 journals. TelDB is part of GenLink, an NIH-funded resource headed by researchers at Washington University at St. Louis. There has been a recent finding regarding telomerase, a gene which affects the mechanisms controlling human cell replication. The site above provides general information on telomerase, current telomere research, and the use of telemorase in medical practice. Telomerase increases the life-span of a cell, and is thus central to both aging and cancer.

1995-01-01

55

Meloneis Gen. Nov., a New Epipsammic Genus of Rhaphoneidaceae (Bacillariophyceae)  

PubMed Central

The diatom family Rhaphoneidaceae is characterized by high generic diversity and low species diversity with most genera known to have long stratigraphic ranges. The genera within this family are neritic marine, and mostly epipsammic. A new modern and epipsammic genus, Meloneis gen. nov., is described herein and is compared to all genera within Rhaphoneidaceae and especially to Rhaphoneis Ehrenberg s.l. Within Meloneis three new species and one variety are distinguished and described herein: M. mimallis sp. nov., M. mimallis var. zephyria var. nov., M. akytos sp. nov., and M. gorgis sp. nov. PMID:22442663

Louvrou, Ioanna; Danielidis, Daniel B.; Economou-Amilli, Athena

2012-01-01

56

Hunting for new restriction enzymes in GenBank  

SciTech Connect

Restriction enzyme genes are hard to identify unless their surrounding sequences are available. This is because the best definition of a restriction enzyme gene is an open reading frame, that looks like nothing else in GenBank, but lies close to a DNA methylase gene. There are other clues too, such as nearby reading frames that code control proteins or the DNA specificity subunits of Type I restriction enzymes. We are developing software that searches the daily updates of GenBank to find candidate restriction enzyme genes. This is being followed by bench experiments to see of the predictions are correct. More than 50 potential new restriction enzymes have been predicted and it is quite remarkable that the density of restriction enzyme genes in microbial DNA is greater than one system per 200 Kb. The software development is emphasizing the graphic presentation of the search results. The approach could be used for other situations where a molecular biologist is interested to find new examples of their favorite genes.

Roberts, R.J. [New England Biolabs, Inc., Beverly, MA (United States)

1997-12-01

57

GenGIS: A geospatial information system for genomic data  

PubMed Central

The increasing availability of genetic sequence data associated with explicit geographic and ecological information is offering new opportunities to study the processes that shape biodiversity. The generation and testing of hypotheses using these data sets requires effective tools for mathematical and visual analysis that can integrate digital maps, ecological data, and large genetic, genomic, or metagenomic data sets. GenGIS is a free and open-source software package that supports the integration of digital map data with genetic sequences and environmental information from multiple sample sites. Essential bioinformatic and statistical tools are integrated into the software, allowing the user a wide range of analysis options for their sequence data. Data visualizations are combined with the cartographic display to yield a clear view of the relationship between geography and genomic diversity, with a particular focus on the hierarchical clustering of sites based on their similarity or phylogenetic proximity. Here we outline the features of GenGIS and demonstrate its application to georeferenced microbial metagenomic, HIV-1, and human mitochondrial DNA data sets. PMID:19635847

Parks, Donovan H.; Porter, Michael; Churcher, Sylvia; Wang, Suwen; Blouin, Christian; Whalley, Jacqueline; Brooks, Stephen; Beiko, Robert G.

2009-01-01

58

Mutation and association analysis of GEN1 in breast cancer susceptibility.  

PubMed

GEN1 was recently identified as a key Holliday junction resolvase involved in homologous recombination. Somatic truncating GEN1 mutations have been reported in two breast cancers. Together these data led to the proposition that GEN1 is a breast cancer predisposition gene. In this article we have formally investigated this hypothesis. We performed full-gene mutational analysis of GEN1 in 176 BRCA1/2-negative familial breast cancer samples and 159 controls. We genotyped six SNPs tagging the 30 common variants in the transcribed region of GEN1 in 3,750 breast cancer cases and 4,907 controls. Mutation analysis revealed one truncating variant, c.2515_2519delAAGTT, which was present in 4% of cases and 4% of controls. We identified control individuals homozygous for the deletion, demonstrating that the last 69 amino acids of GEN1 are dispensable for its function. We identified 17 other variants, but their frequency did not significantly differ between cases and controls. Analysis of 3,750 breast cancer cases and 4,907 controls demonstrated no evidence of significant association with breast cancer for six SNPs tagging the 30 common GEN1 variants. These data indicate that although it also plays a key role in double-strand DNA break repair, GEN1 does not make an appreciable contribution to breast cancer susceptibility by acting as a high- or intermediate-penetrance breast cancer predisposition gene like BRCA1, BRCA2, CHEK2, ATM, BRIP1 and PALB2 and that common GEN1 variants do not act as low-penetrance susceptibility alleles analogous to SNPs in FGFR2. Furthermore, our analyses demonstrate the importance of undertaking appropriate genetic investigations, typically full gene screening in cases and controls together with large-scale case-control association analyses, to evaluate the contribution of genes to cancer susceptibility. PMID:20512659

Turnbull, Clare; Hines, Sarah; Renwick, Anthony; Hughes, Deborah; Pernet, David; Elliott, Anna; Seal, Sheila; Warren-Perry, Margaret; Gareth Evans, D; Eccles, Diana; Stratton, Michael R; Rahman, Nazneen

2010-11-01

59

Decay heat removal in GEN IV gas cooled fast reactors.  

SciTech Connect

The safety goal of the current designs of advanced high-temperature thermal gas-cooled reactors (HTRs) is that no core meltdown would occur in a depressurization event with a combination of concurrent safety system failures. This study focused on the analysis of passive decay heat removal (DHR) in a GEN IV direct-cycle gas-cooled fast reactor (GFR) which is based on the technology developments of the HTRs. Given the different criteria and design characteristics of the GFR, an approach different from that taken for the HTRs for passive DHR would have to be explored. Different design options based on maintaining core flow were evaluated by performing transient analysis of a depressurization accident using the system code RELAP5-3D. The study also reviewed the conceptual design of autonomous systems for shutdown decay heat removal and recommends that future work in this area should be focused on the potential for Brayton cycle DHRs.

Cheng, L. Y.; Wei, T. Y. C. (Nuclear Engineering Division); (BNL)

2009-08-01

60

PopGen: A virtual human population generator.  

PubMed

The risk assessment of environmental chemicals and drugs is moving towards a paradigm shift in approach which seeks the full replacement animal testing with high throughput, mechanistic, in vitro systems. This new vision will be reliant on the measurement in vitro, of concentration-dependent responses where prolonged excessive perturbations of specific biochemical pathways are likely to lead to adverse health effects in an intact organism. Such an approach requires a framework, into which disparate data generated using in vitro, in silico and in chemico systems, can be integrated and utilised for quantitative in vitro-to-in vivo extrapolation (QIVIVE), ultimately to the human population level. Physiologically based pharmacokinetic (PBPK) models are ideally suited for this and are obligatory in order to translate in vitro concentration-response relationships to an exposure or dose, route and duration regime in people. In this report we describe PopGen, a virtual human population generator which is a user friendly, open access web-based application for the prediction of realistic anatomical, physiological and phase 1 metabolic variation in a wide range of healthy human populations. We demonstrate how PopGen can be used for QIVIVE by providing input to a PBPK model, at an appropriate level of detail, to reconstruct exposure from human biomonitoring data. We discuss how the process of exposure reconstruction from blood biomarkers, in general, is analogous to exposure or dose reconstruction from concentration-response measurements made in proposed in vitro cell based systems which are assumed to be surrogates for target organs. PMID:23876857

McNally, Kevin; Cotton, Richard; Hogg, Alex; Loizou, George

2014-01-01

61

Wigginsiella n. gen., spongodinium, and Apteodinium as members of the aptianaventriosum complex (fossil dinophyceae)  

Microsoft Academic Search

Well?preserved representatives of three genera of fossil gonyaulacoid dinoflagellate cysts, Wigginsiella n. gen., Spongodinium Deflandre 1935, and Apteodinium Eisenack 1958, show paratabulation details that indicate a close relationship to genera referred to the \\

1987-01-01

62

USDA Forest Service Gen. Tech. Rep. PSW-110. 1989. 347 SESSION H: EFFECTS OF STREAM DIVERSIONS  

E-print Network

USDA Forest Service Gen. Tech. Rep. PSW-110. 1989. 347 SESSION H: EFFECTS OF STREAM DIVERSIONS to water resources, for agriculture and to assist in mining. In more recent times, water in montane areas

Standiford, Richard B.

63

GenBrick – A Rapid Multi-Part Assembly Method for BioBricks  

E-print Network

This BioBricks Foundation Request for Comments (BBF RFC) describes a novel approach, GenBrick, for the rapid assembly of multiple BioBrick RFC10-compatible parts in a single reaction, with completely flexible part order, ...

Gasi?nait?, Lina

2013-10-04

64

Reclassification of species of the spiral-shaped phototrophic purple non-sulfur bacteria of the alpha-Proteobacteria: description of the new genera Phaeospirillum gen. nov., Rhodovibrio gen. nov., Rhodothalassium gen. nov. and Roseospira gen. nov. as well as transfer of Rhodospirillum fulvum to Phaeospirillum fulvum comb. nov., of Rhodospirillum molischianum to Phaeospirillum molischianum comb. nov., of Rhodospirillum salinarum to Rhodovibrio salexigens.  

PubMed

The 165 rDNA sequence of Rhodospirillum mediosalinum was determined and compared with corresponding sequences from other spiral-shaped purple non-sulfur bacteria classified as or related to the genus Rhodospirillum in the alpha subclass of the Proteobacteria. Sequence similarities separate the currently recognized Rhodospirillum species into five different groups with no more than 91% sequence similarity, clearly indicating the necessity to recognize these groups as different genera. Major diagnostic properties of these bacteria are compared and new genera Phaeospirillum gen. nov., Roseospira gen. nov., Rhodothalassium gen. nov. and Rhodovibrio gen. nov. are described with the species Phaeospirillum fulvum comb. nov., Phaeospirillum molischianum comb. nov., Rhodovibrio salinarum comb. nov., Rhodovibrio sodomensis comb. nov., Rhodothalassium salexigens comb. nov. and Roseospira mediosalina comb. nov. The genus Rhodospirillum is represented by Rhodospirillum rubrum and Rhodospirillum photometricum and an emended description of this genus is also given. PMID:9734033

Imhoff, J F; Petri, R; Süling, J

1998-07-01

65

LiGen: a high performance workflow for chemistry driven de novo design.  

PubMed

Tools for molecular de novo design are actively sought incorporating sets of chemical rules for fast and efficient identification of structurally new chemotypes endowed with a desired set of biological properties. In this paper, we present LiGen, a suite of programs which can be used sequentially or as stand-alone tools for specific purposes. In its standard application, LiGen modules are used to define input constraints, either structure-based, through active site identification, or ligand-based, through pharmacophore definition, to docking and to de novo generation. Alternatively, individual modules can be combined in a user-defined manner to generate project-centric workflows. Specific features of LiGen are the use of a pharmacophore-based docking procedure which allows flexible docking without conformer enumeration and accurate and flexible reactant mapping coupled with reactant tagging through substructure searching. The full description of LiGen functionalities is presented. PMID:23617275

Beccari, Andrea R; Cavazzoni, Carlo; Beato, Claudia; Costantino, Gabriele

2013-06-24

66

New records of the Cryphonectriaceae from southern Africa including Latruncellus aurorae gen. sp. nov.  

E-print Network

New records of the Cryphonectriaceae from southern Africa including Latruncellus aurorae gen. sp in Africa. Surveys in the past 3 y in southern Africa have led to the discovery of cankers with fruiting

67

Ferrimicrobium acidiphilum gen. nov., sp. nov. and Ferrithrix thermotolerans gen. nov., sp. nov.: heterotrophic, iron-oxidizing, extremely acidophilic actinobacteria.  

PubMed

Two novel extremely acidophilic, iron-oxidizing actinobacteria were isolated, one from a mine site in North Wales, UK (isolate T23(T)), and the other from a geothermal site in Yellowstone National Park, Wyoming, USA (Y005(T)). These new actinobacteria belong to the subclass Acidimicrobidae, and in contrast to the only other classified member of the subclass (Acidimicrobium ferrooxidans), both isolates were obligate heterotrophs. The mine site isolate was mesophilic and grew as small rods, while the Yellowstone isolate was a moderate thermophile and grew as long filaments, forming macroscopic flocs in liquid media. Both isolates accelerated the oxidative dissolution of pyrite in yeast extract-amended cultures, but neither was able to oxidize reduced forms of sulfur. Ferrous iron oxidation enhanced growth yields of the novel mesophilic actinobacterium T23(T), though this was not confirmed for the Yellowstone isolate. Both isolates catalysed the dissimilatory reduction of ferric iron, using glycerol as electron donor, in oxygen-free medium. Based on comparative analyses of base compositions of their chromosomal DNA and of their 16S rRNA gene sequences, the isolates are both distinct from each other and from Acidimicrobium ferrooxidans, and are representatives of two novel genera. The names Ferrimicrobium acidiphilum gen. nov., sp. nov. and Ferrithrix thermotolerans gen. nov., sp. nov. are proposed for the mesophilic and moderately thermophilic isolates, respectively, with the respective type strains T23(T) (=DSM 19497(T)=ATCC BAA-1647(T)) and Y005(T) (=DSM 19514(T)=ATCC BAA-1645(T)). PMID:19406797

Johnson, D Barrie; Bacelar-Nicolau, Paula; Okibe, Naoko; Thomas, Angharad; Hallberg, Kevin B

2009-05-01

68

Characterization of Romboutsia ilealis gen. nov., sp. nov., isolated from the gastro-intestinal tract of a rat, and proposal for the reclassification of five closely related members of the genus Clostridium into the genera Romboutsia gen. nov., Intestinibacter gen. nov., Terrisporobacter gen. nov. and Asaccharospora gen. nov.  

PubMed

A Gram-positive staining, rod-shaped, non-motile, spore-forming obligately anaerobic bacterium, designated CRIBT, was isolated from the gastro-intestinal tract of a rat and characterized. The major cellular fatty acids of strain CRIBT were saturated and unsaturated straight-chain C12-C19 fatty acids, with C16:0 being the predominant fatty acid. The polar lipid profile comprised six glycolipids, four phospholipids and one lipid that did not stain with any of the specific spray reagents used. The only quinone was MK-6. The predominating cell-wall sugars were glucose and galactose. The peptidoglycan type of strain CRIBT was A1? lanthionine-direct. The genomic DNA G+C content of strain CRIBT was 28.1 mol%. On the basis of 16S rRNA gene sequence similarity, strain CRIBT was most closely related to a number of species of the genus Clostridium, including Clostridium lituseburense (97.2%), Clostridium glycolicum (96.2%), Clostridium mayombei (96.2%), Clostridium bartlettii (96.0%) and Clostridium irregulare (95.5%). All these species show very low 16S rRNA gene sequence similarity (<85%) to the type strain of Clostridium butyricum, the type species of the genus Clostridium. DNA-DNA hybridization with closely related reference strains indicated reassociation values below 32%. On the basis of phenotypic and genetic studies, a novel genus, Romboutsia gen. nov., is proposed. The novel isolate CRIBT (=DSM 25109T=NIZO 4048T) is proposed as the type strain of the type species, Romboutsia ilealis gen. nov., sp. nov., of the proposed novel genus. It is proposed that C. lituseburense is transferred to this genus as Romboutsia lituseburensis comb. nov. Furthermore, the reclassification into novel genera is proposed for C. bartlettii, as Intestinibacter bartlettii gen. nov., comb. nov. (type species of the genus), C. glycolicum, as Terrisporobacter glycolicus gen. nov., comb. nov. (type species of the genus), C. mayombei, as Terrisporobacter mayombei gen. nov., comb. nov., and C. irregulare, as Asaccharospora irregularis gen. nov., comb. nov. (type species of the genus), on the basis of additional data collected in this study. In addition, an emendation of the species Peptostreptococcus anaerobius and the order Eubacteriales is provided. PMID:24480908

Gerritsen, Jacoline; Fuentes, Susana; Grievink, Wieke; van Niftrik, Laura; Tindall, Brian J; Timmerman, Harro M; Rijkers, Ger T; Smidt, Hauke

2014-05-01

69

Bietet das NexGen LPS Flex mobile-Knieprothesen- system Vorteile gegenüber dem NexGen LPS? - Ein Vergleich klinischer und radiologischer Ergebnisse  

Microsoft Academic Search

Under experimental conditions, mobile bearing knee prostheses have several advantages. The optimized congruence of the tibio- femoral joint surface allows a knee flexion of more than 1208 without creating instability or increase of wear. Aim: The aim of this study is to compare the results of a prospective randomized study after implantation of the mobile bearing knee prosthesis NexGen LPS

D. Wohlrab; J. Ditl; R. Herrschelmann; U. Schietsch; W. Hein; R. Hube

2005-01-01

70

Puniceibacterium antarcticum gen. nov., sp. nov., isolated from seawater.  

PubMed

A Gram-reaction-negative, aerobic, non-flagellated, rod-shaped bacterium, designated strain SM1211T, was isolated from Antarctic seawater. The isolate grew at 4-35 °C and with 0-10% (w/v) NaCl. It could produce bacteriochlorophyll a, but did not reduce nitrate to nitrite or hydrolyse DNA. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain SM1211T constituted a distinct phylogenetic line within the family Rhodobacteraceae and was closely related to species in the genera Litorimicrobium, Leisingera, Seohaeicola and Phaeobacter with 95.1-96.0% similarities. The predominant cellular fatty acid was C18:1?7c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid and two unidentified phospholipids. The genomic DNA G+C content of strain SM1211T was 60.7 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain SM1211T is considered to represent a novel species in a new genus within the family Rhodobacteraceae, for which the name Puniceibacterium antarcticum gen. nov., sp. nov. is proposed. The type strain of Puniceibacterium antarcticum is SM1211T (=CCTCC AB 2013147T=KACC 16875T). PMID:24478211

Liu, Chang; Zhang, Xi-Ying; Su, Hai-Nan; Zhou, Ming-Yang; Chen, Bo; Li, Hai; Chen, Xiu-Lan; Zhao, Dian-Li; Zhou, Bai-Cheng; Shi, Mei; Zhang, Yu-Zhong

2014-05-01

71

Pisciglobus halotolerans gen. nov., sp. nov., isolated from fish sauce.  

PubMed

Two strains of Gram-stain-positive, catalase-negative, tetrad-forming cocci, C01(T) and C02, were isolated in Thailand from fish sauce. They were facultatively anaerobic, non-motile and non-spore-forming bacteria. These strains produced l-lactic acid from glucose. They grew at pH 5.0-9.0, at 15-40 °C and in the presence of 10?% (w/v) NaCl. The dominant fatty acid was C(18?:?1)?9c. The DNA G+C contents of strains C01(T) and C02 were 38.6 and 38.7 mol%, respectively. Strain C01(T) was related most closely to Desemzia incerta DSM 20581(T), with a 16S rRNA gene sequence similarity of 96.9?%. The strains could be distinguished clearly from D. incerta DSM 20581(T) based on cell morphology, physiological and biochemical characteristics and low levels of DNA-DNA relatedness. On the basis of the data presented, strains C01(T) and C02 are considered to represent a novel species of a new genus in the Bacillus-Lactobacillus cluster, for which the name Pisciglobus halotolerans gen. nov., sp. nov. is proposed. The type strain of Pisciglobus halotolerans is C01(T) (?=?KCTC 13150(T) ?=?TISTR 1958(T) ?=?PCU 316(T)). PMID:20729308

Tanasupawat, Somboon; Thongsanit, Jaruwan; Thawai, Chitti; Lee, Keun Chul; Lee, Jung-Sook

2011-07-01

72

Initial Investigation of Operational Concept Elements for NASA's NextGen-Airportal Project Research  

NASA Technical Reports Server (NTRS)

The NextGen-Airportal Project is organized into three research focus areas: Safe and Efficient Surface Operations, Coordinated Arrival/Departure Operations Management, and Airportal Transition and Integration Management. The content in this document was derived from an examination of constraints and problems at airports for accommodating future increases in air traffic, and from an examination of capabilities envisioned for NextGen. The concepts are organized around categories of constraints and problems and therefore do not precisely match, but generally reflect, the research focus areas. The concepts provide a framework for defining and coordinating research activities that are, and will be, conducted by the NextGen-Airportal Project. The concepts will help the research activities function as an integrated set focused on future needs for airport operations and will aid aligning the research activities with NextGen key capabilities. The concepts are presented as concept elements with more detailed sub-elements under each concept element. For each concept element, the following topics are discussed: constraints and problems being addressed, benefit descriptions, required technology and infrastructure, and an initial list of potential research topics. Concept content will be updated and more detail added as the research progresses. The concepts are focused on enhancing airportal capacity and efficiency in a timeframe 20 to 25 years in the future, which is similar to NextGen's timeframe.

Lohr, Gary; Lee, Jonathan; Poage, James L.; Tobias, Leonard

2009-01-01

73

ProGenExpress: Visualization of quantitative data on prokaryotic genomes  

PubMed Central

Background The integration of genomic information with quantitative experimental data is a key component of systems biology. An increasing number of microbial genomes are being sequenced, leading to an increasing amount of data from post-genomics technologies. The genomes of prokaryotes contain many structures of interest, such as operons, pathogenicity islands and prophage sequences, whose behaviour is of interest during infection and disease. There is a need for simple and novel tools to display and analyse data from these integrated datasets, and we have developed ProGenExpress as a tool for visualising arbitrarily complex numerical data in the context of prokaryotic genomes. Results Here we describe ProGenExpress, an R package that allows researchers to easily and quickly visualize quantitative measurements, such as those produced by microarray experiments, in the context of the genome organization of sequenced prokaryotes. Data from microarrays, proteomics or other whole-genome technologies can be accurately displayed on the genome. ProGenExpress can also search for novel regions of interest that consist of groups of adjacent genes that show similar patterns across the experimental data set. We demonstrate ProGenExpress with microarray data from a time-course experiment involving Salmonella typhimurium. Conclusion ProGenExpress can be used to visualize quantitative data from complex experiments in the context of the genome of sequenced prokaryotes, and to find novel regions of interest. PMID:15829007

Watson, Michael

2005-01-01

74

Safety Sufficiency for NextGen: Assessment of Selected Existing Safety Methods, Tools, Processes, and Regulations  

NASA Technical Reports Server (NTRS)

NextGen is a complex socio-technical system and, in many ways, it is expected to be more complex than the current system. It is vital to assess the safety impact of the NextGen elements (technologies, systems, and procedures) in a rigorous and systematic way and to ensure that they do not compromise safety. In this study, the NextGen elements in the form of Operational Improvements (OIs), Enablers, Research Activities, Development Activities, and Policy Issues were identified. The overall hazard situation in NextGen was outlined; a high-level hazard analysis was conducted with respect to multiple elements in a representative NextGen OI known as OI-0349 (Automation Support for Separation Management); and the hazards resulting from the highly dynamic complexity involved in an OI-0349 scenario were illustrated. A selected but representative set of the existing safety methods, tools, processes, and regulations was then reviewed and analyzed regarding whether they are sufficient to assess safety in the elements of that OI and ensure that safety will not be compromised and whether they might incur intolerably high costs.

Xu, Xidong; Ulrey, Mike L.; Brown, John A.; Mast, James; Lapis, Mary B.

2013-01-01

75

USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 811 Sampling Methods for Snags and Large  

E-print Network

USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 811 Sampling Methods for Snags and LargeGrande, OR 97850. #12;Snag Sampling Methods--Bate, Garton, and Wisdom USDA Forest Service Gen. Tech. Rep. PSW sampling methods. In response to this need, we produced a Forest Service General Technical Report (GTR

Standiford, Richard B.

76

A Rapid Micro Polymerase Chain Reaction System (GenSpector Micro PCR) for Hepatitis B Virus DNA Detection  

E-print Network

A Rapid Micro Polymerase Chain Reaction System (GenSpector® Micro PCR) for Hepatitis B Virus DNA a rapid micro PCR (polymerase chain reaction) system (GenSpector® Micro PCR) for the application of Technology, PO Box 111, Suwon 440-600, Korea Abstract This paper presents a rapid micro PCR (polymerase chain

Oh, Kwang W.

77

Critical Issues on Materials for Gen-IV Reactors  

SciTech Connect

Within the LDRD on 'Critical Issues on Materials for Gen-IV Reactors' basic thermodynamics of the Fe-Cr alloy and accurate atomistic modeling were used to help develop the capability to predict hardening, swelling and embrittlement using the paradigm of Multiscale Materials Modeling. Approaches at atomistic and mesoscale levels were linked to build-up the first steps in an integrated modeling platform that seeks to relate in a near-term effort dislocation dynamics to polycrystal plasticity. The requirements originated in the reactor systems under consideration today for future sources of nuclear energy. These requirements are beyond the present day performance of nuclear materials and calls for the development of new, high temperature, radiation resistant materials. Fe-Cr alloys with 9-12% Cr content are the base matrix of advanced ferritic/martensitic (FM) steels envisaged as fuel cladding and structural components of Gen-IV reactors. Predictive tools are needed to calculate structural and mechanical properties of these steels. This project represents a contribution in that direction. The synergy between the continuous progress of parallel computing and the spectacular advances in the theoretical framework that describes materials have lead to a significant advance in our comprehension of materials properties and their mechanical behavior. We took this progress to our advantage and within this LDRD were able to provide a detailed physical understanding of iron-chromium alloys microstructural behavior. By combining ab-initio simulations, many-body interatomic potential development, and mesoscale dislocation dynamics we were able to describe their microstructure evolution. For the first time in the case of Fe-Cr alloys, atomistic and mesoscale were merged and the first steps taken towards incorporating ordering and precipitation effects into dislocation dynamics (DD) simulations. Molecular dynamics (MD) studies of the transport of self-interstitial, vacancy and point defect clusters in concentrated Fe-Cr alloys were performed for future diffusion data calculations. A recently developed parallel MC code with displacement allowed us to predict the evolution of the defect microstructures, local chemistry changes, grain boundary segregation and precipitation resulting from radiation enhanced diffusion. We showed that grain boundaries, dislocations and free surfaces are not preferential for alpha-prime precipitation, and explained experimental observations of short-range order (SRO) in Fe-rich FeCr alloys. Our atomistic studies of dislocation hardening allowed us to obtain dislocation mobility functions for BCC pure iron and Fe-Cr and determine for FCC metals the dislocation interaction with precipitates with a description to be used in Dislocation Dynamic (DD) codes. A Synchronous parallel Kinetic Monte Carlo code was developed and tested which promises to expand the range of applicability of kMC simulations. This LDRD furthered the limits of the available science on the thermodynamic and mechanic behavior of metallic alloys and extended the application of physically-based multiscale materials modeling to cases of severe temperature and neutron fluence conditions in advanced future nuclear reactors. The report is organized as follows: after a brief introduction, we present the research activities, and results obtained. We give recommendations on future LLNL activities that may contribute to the progress in this area, together with examples of possible research lines to be supported.

Caro, M; Marian, J; Martinez, E; Erhart, P

2009-02-27

78

HIV gp120 vaccine - VaxGen: AIDSVAX, AIDSVAX B/B, AIDSVAX B/E, HIV gp120 vaccine - Genentech, HIV gp120 vaccine AIDSVAX - VaxGen, HIV vaccine AIDSVAX - VaxGen.  

PubMed

VaxGen is developing prophylactic vaccines against HIV-1 consisting of two recombinant gp120 surface proteins from different HIV-1 strains.This profile has been selected from R&D Insight, a pharmaceutical intelligence database produced by Adis International Ltd. The bivalent vaccines [AIDSVAX B/B and AIDSVAX B/E] are being evaluated in two phase III trials. The first multicentre phase III trial of AIDSVAX B/B, was conducted principally in Canada and the US but also at some sites in the Netherlands and Puerto Rico. The trial was completed at the end of 2002. The second phase III trial is being conducted in Thailand with the AIDSVAX B/E vaccine. VaxGen announced in July 2002 that it would be delaying its Biologics License Application (BLA) for AIDSVAX until 2004 to enable the company to fulfil pre-approval manufacturing requirements. AIDSVAX is based on an earlier monovalent gp120 vaccine developed by Genentech that was shown to be safe in humans. VaxGen (formerly Genenvax) was formed as a spin-off company from Genentech with the sole purpose of developing the gp120 vaccine. VaxGen announced in July 2002 that the original License and Supply agreement with Genentech, signed in May 1997, had been amended. Under the revised agreement, Genentech maintains its right to market and sell AIDSVAX in North America, but has relinquished its options to commercialise the vaccine candidate in the rest of the world. Genentech's earlier decision to waive its option to manufacture AIDSVAX has also been formalised in this agreement. Additionally, VaxGen's royalty payments to Genentech for sales to the WHO or UN for underdeveloped nations have also been reduced by up to 50% and Genentech has extended the milestone date associated with VaxGen submitting an NDA. A $US120 million joint venture (Celltrion) has been formed between VaxGen and South Korean investors to manufacture more than 200 million doses of AIDSVAX a year. Celltrion will build and operate two biotechnology manufacturing facilities: a pilot plant in South San Francisco and a larger plant in Incheon, South Korea. VaxGen will retain a 44% interest in the new company, as well as any profit generated by the AIDS vaccine. If AIDSVAX wins regulatory approval, VaxGen is committed to purchasing a minimum of 87 million doses a year. Celltrion announced in July 2002 that it had acquired 24 acres of land in Incheon, South Korea, for the site of its major biologics manufacturing facility. The facility is scheduled to be ready for commercial operation by 2005. The US FDA granted fast-track designations to the two vaccines AIDSVAX B/B and AIDSVAX B/E in December 2002. The study volunteers included 5108 men who have sex with men and 309 at-risk women, all of whom were meant to be HIV negative when they joined the trial. During the 36-month trial, a total of seven injections were administered at months 0, 1, 6, 12, 18, 24 and 30. The ratio of vaccine to placebo recipients was 2:1. On February 24 2003, VaxGen announced that AIDSVAX B/B did not prove effective in the trials conducted in North America and Europe. The study did not show a statistically significant reduction of HIV infection within the study population as a whole, which was the primary endpoint of the trial. However, the study did show a statistically significant reduction of HIV infection in certain vaccinated groups. Trial data indicate that black and Asian volunteers appeared to produce higher levels of antibodies against HIV. White and Hispanic volunteers appeared to develop consistently lower levels of protective antibodies following vaccination. VaxGen intends to conduct additional analyses to confirm if there was a direct correlation between the level of antibodies and the prevention of infection. The company intends to continue development of the vaccine through licensure, including any studies necessary to evaluate the protective riticism in the media about the statistical analysis of the non-Caucasian data, VaxGen issued a statement on 27 February 2003 claiming that the analysis of data from the trial followed a statistica

2003-01-01

79

Rudaibacter terrae gen. nov., sp. nov., isolated from greenhouse soil.  

PubMed

A novel Gram-stain-positive, non-motile, rod-shaped bacterium, designated 5GHs34-4(T), was isolated from greenhouse soil in Yongin, Republic of Korea. Growth occurred in the temperature range of 10-37 °C (optimum 28-30 °C) and at pH 5.0-9.0 (optimum pH 7.0). It can tolerate up to 3?% (w/v) NaCl. The strain showed 16S rRNA gene sequence similarity levels of 95.1-97.0?% with species of the genus Leifsonia, 95.7-96.7?% with species of the genus Herbiconiux, 95.1-96.4?% with species of the genus Salinibacterium and 96.1?% with Labedella gwakjiensis and Homoserinimonas aerilata. The highest sequence similarities (97.0?%) were with Leifsonia aquatica JCM 1368(T), Leifsonia poae VKM Ac-1401(T) and Leifsonia psychrotolerans LI1(T). The peptidoglycan type determined for strain 5GHs34-4(T) was B2? with dl-2,4-diaminobutyric acid at position 3. The murein was of the acetyl type. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The menaquinones detected were MK-13, MK-12 and MK-14, and the major fatty acids were summed feature 8 (C18?:?1?7c and/or C18?:?1?6c), anteiso-C17?:?0 and anteiso-C15?:?0. The phenotypic and phylogenetic traits of strain 5GHs34-4(T) differed in some respects from those of members of the family Microbacteriaceae. Therefore, strain 5GHs34-4(T) is considered to represent a novel species of a new genus in the family Microbacteriaceae, for which the name Rudaibacter terrae gen. nov., sp. nov. is proposed. The type strain is 5GHs34-4(T) (?=?KACC 15523(T)?=?NBRC 108754(T)). PMID:23728372

Kim, Soo-Jin; Moon, Ji-Young; Hamada, Moriyuki; Tamura, Tomohiko; Weon, Hang-Yeon; Suzuki, Ken-ichiro; Kwon, Soon-Wo

2013-11-01

80

Fusicatenibacter saccharivorans gen. nov., sp. nov., isolated from human faeces.  

PubMed

Three Gram-stain-positive, obligately anaerobic, non-motile, non-spore-forming, spindle-shaped bacterial strains (HT03-11(T), KO-38 and TT-111), isolated from human faeces were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing showed that the strains were highly related to each other genetically (displaying >99?% sequence similarity) and represented a previously unknown subline within the Blautia coccoides rRNA group of organisms (cluster XIVa). The closest phylogenetic neighbours of strain HT03-11(T) were Clostridium bolteae WAL 16351(T) (93.7?% 16S rRNA gene sequence similarity) and Clostridium saccharolyticum WM1(T) (93.7?% similarity). All isolates produced lactic acid, formic acid, acetic acid and succinic acid as fermentation end products from glucose. Their chemotaxonomic properties included lysine as the cell wall diamino acid and C16?:?0, C18?:?1?7c DMA and C16?:?0 DMA as the major fatty acids. The G+C contents of the genomic DNA were 46.9-47.2 mol% (HPLC). Several phenotypic and chemotaxonomic characteristics could be readily used to differentiate the isolates from phylogenetically related clostridia. Therefore, strains HT03-11(T), KO-38 and TT-111 represent a novel species in a new genus of the family Lachnospiraceae, for which the name Fusicatenibacter saccharivorans gen. nov., sp. nov. is proposed. The type strain of the type species is HT03-11(T) (?=?YIT 12554(T)?=?JCM 18507(T)?=?DSM 26062(T)). PMID:23625266

Takada, Toshihiko; Kurakawa, Takashi; Tsuji, Hirokazu; Nomoto, Koji

2013-10-01

81

LabSystem Gen, a tool for structuring and analyzing genetic data in histocompatibility laboratories.  

PubMed

Analysis of HLA data involves queries on web portals, whose search parameters are data stored in laboratories' databases. In order to automate these queries, one approach is to structure laboratory data into a database and to develop bioinformatic tools to perform the data mapping. In this context, we developed the LabSystem Gen tool that allows users to create a Laboratory Information System, without programming. Additionally we implemented a framework that provides bioinformatic tools, transparent access to public HLA (human leukocyte antigen) information resources. We demonstrated the LabSystemGen system by implementing BMDdb, which is a LIMS that manages data of recipients and donors of organ transplant. PMID:22316634

Sousa, Luiz Cláudio Demes da Mata; dos Santos Neto, Pedro de Alcântara; de Souza, Fernando da Fonseca; do Monte, Semiramis Jamil Hadad

2012-04-01

82

Batwanema gen. n. and Chokwenema gen. n. (Oxyurida, Hystrignathidae), new nematode genera as parasites of Passalidae (Coleoptera) from the Democratic Republic of Congo  

PubMed Central

Abstract Two new genera and species parasitizing passalid beetles from the Democratic Republic of Congo are described. Batwanema congo gen. n. et sp. n. is characterized by having females with the cervical cuticle armed with scale-like projections, arranged initially in rows of eight elements that gradually divide and form pointed spines toward the end of the spiny region, two cephalic annuli, clavate procorpus and genital tract monodelphic-prodelphic. Two Malagasian species of Artigasia Christie, 1934 were placed in this genus as B. latum (Van Waerebeke, 1973) comb. n. and B. annulatum (Van Waerebeke, 1973) comb. n. Chokwenema lepidophorum gen. n. et sp. n. is characterized by having females with the cervical cuticle armed with scale-like projections, arranged initially in rows of eight elements (similar to Batwanema) that divide gradually, forming spines; a single cephalic annule cone-like, truncated, moderately inflated; procorpus sub-cylindrical and genital tract didelphic-amphidelphic. PMID:24363593

Morffe, Jans; Garcia, Nayla

2013-01-01

83

PZT piezoelectric films on glass for Gen-X imaging  

NASA Astrophysics Data System (ADS)

The proposed adaptive optics system for the Gen-X telescope uses piezoelectric lead zirconate titanate (PZT) films deposited on flexible glass substrates. The low softening transition of the glass substrates imposes several processing challenges that require the development of new approaches to deposit high quality PZT thin films. Synthesis and optimization of chemical solution deposited 1 ?m thick films of PbZr0.52Ti0.48O3 on small area (1 in2) and large area (16 in2) Pt/Ti/glass substrates has been performed. In order to avoid warping of the glass at temperatures typically used to crystallize PZT films ({700°C), a lower temperature, two-step crystallization process was employed. An {80 nm thick seed layer of PbZr0.30Ti0.70O3 was deposited to promote the growth of the perovskite phase. After the deposition of the seed layer, the films were annealed in a rapid thermal annealing (RTA) furnace at 550°C for 3 minutes to nucleate the perovskite phase. This was followed by isothermal annealing at 550°C for 1 hour to complete crystallization. For the subsequent PbZr0.52Ti0.48O3 layers, the same RTA protocol was performed, with the isothermal crystallization implemented following the deposition of three PbZr0.52Ti0.48O3 spin-coated layers. Over the frequency range of 1 kHz to 100 kHz, films exhibit relative permittivity values near 800 with loss tangents below 0.07. Hysteresis loops show low levels of imprint with coercive fields of 40-50 kV/cm in the forward direction and 50-70 kV/cm in the reverse direction. The remanent polarization varied from 25-35 ?C/cm2 and e31,f values were approximately -5.0 C/m2. In scaling up the growth procedure to large area films, where warping becomes more pronounced due to the increased size of the substrate, the pyrolysis and crystallization conditions were performed in a box furnace to improve the temperature uniformity. By depositing films on both sides of the glass substrate, the tensile stresses are balanced, providing a sufficiently flat surface to continue PZT deposition. The properties of the large area film are comparable to those obtained on small substrates. While sol-gel processing is a viable approach to the deposition of high quality PZT thin films on glass substrates, preliminary results using RF magnetron sputter deposition demonstrate comparable properties with a significantly simpler process that offers a superior route for large scale production.

Wilke, Rudeger H. T.; Trolier-McKinstry, Susan; Reid, Paul B.; Schwartz, Daniel A.

2010-09-01

84

Microcetus lappus gen. nov., sp. nov.: new species of ciliated protozoon from the bovine rumen.  

PubMed Central

A new species of small, ciliated protozoon, Microcetus lappus gen. nov., sp. nov., from the rumen of Norwegian Red cattle is described. M. lappus possesses a novel cytopharyngeal apparatus of two rod-shaped structures, one situated on the dorsal side of the buccal cavity and one on the ventral side, suggesting that it belongs to a previously undescribed taxon. Images PMID:3094449

Orpin, C G; Mathiesen, S D

1986-01-01

85

FutureGen: Pathway to Near-Zero Emissions and Sustainable Energy  

SciTech Connect

This presentation will highlight the U.S. Department of Energy’s (DOE) FutureGen project ? a $1 billion government-industry partnership to design, build, and operate a near-zero emissions coal-fueled power plant. The lead organization for the FutureGen initiative is the National Energy Technology Laboratory (NETL), a multi-purpose laboratory operated by the U.S. DOE’s Office of Fossil Energy. NETL has a mission to conduct R&D from fundamental science to technology demonstration for resolving the environmental, supply, and reliability constraints of producing and using fossil energy resources. The commercial-scale FutureGen R&D facility is a pathway toward future fossil-energy power plants that will produce hydrogen and electricity while nearly eliminating emissions, including carbon dioxide. The 275-megawatt FutureGen plant will initiate operations around 2012 and employ advanced coal gasification technology integrated with combined cycle electricity generation, hydrogen production, and carbon capture and sequestration. Low carbon emissions would be achieved by integrating CO2 capture and sequestration operations with the power plant.

Zitney, S.E.; Sarkus, T.A

2007-11-04

86

A Logico-Structural, Worldview Analysis of the Interrelationship between Science Interest, Gen-  

E-print Network

1 A Logico-Structural, Worldview Analysis of the Interrelationship between Science Interest, Gen was to provide information about gender-related worldview struc- tures. This was an exploratory investigation that sought to identify potential presuppositions in a sin- gle worldview category, the NonSelf, and specifi

Cobern, William W.

87

SIMILASCAROPHIS N. GEN. N. SPP. (NEMATODA: CYSTIDICOLIDAE) PARASITIZING MARINE FISHES OFF THE CHILEAN COAST  

Microsoft Academic Search

Similascarophis (Cystidicolidae) n. gen. is proposed. In the mouth of specimens of this genus, submedial labia are absent and pseudolabia do not have any part projecting toward the central oral opening. These nematodes were obtained from the alimentary tract of 7 marine fish species along the coast of Chile: Bovichthys chilensis Regan, Eleginops maclovinus(Cuvier), Pinguipes chilensis (Valenciennes), Cilus gilberti (Abbott),

Gabriela Muñoz; María Teresa González; Mario George-Nascimento

2004-01-01

88

USDA Forest Service Gen. Tech. Rep. PSW-110. 1989. 519 SESSION K: COORDINATING INTEREST GROUPS  

E-print Network

USDA Forest Service Gen. Tech. Rep. PSW-110. 1989. 519 SESSION K: COORDINATING INTEREST GROUPS interest than it is with riparian environments of forested lands. Duncan Patton explains how riparian's disappearing riparian systems. Dana L. Abell University of California, Davis #12;

Standiford, Richard B.

89

Data Form Number and Name Responsible Office(s) CIHE Data Form Gen  

E-print Network

N E A S C D A T A F O R M S #12;Data Form Number and Name Responsible Office(s) CIHE Data Form Gen: General Information Form President's Office CIHE Data Form 1: Statement of Financial Position Executive Vice President CIHE Data Form 2-1: Statement of Unrestricted Revenues and Expenses Executive Vice

Snider, Barry B.

90

Extending Validated Human Performance Models to Explore NextGen Concepts  

NASA Technical Reports Server (NTRS)

To meet the expected increases in air traffic demands, NASA and FAA are researching and developing Next Generation Air Transportation System (NextGen) concepts. NextGen will require substantial increases in the data available to pilots on the flight deck (e.g., weather,wake, traffic trajectory predictions, etc.) to support more precise and closely coordinated operations (e.g., self-separation, RNAV/RNP, and closely spaced parallel operations, CSPOs). These NextGen procedures and operations, along with the pilot's roles and responsibilities, must be designed with consideration of the pilot's capabilities and limitations. Failure to do so will leave the pilots, and thus the entire aviation system, vulnerable to error. A validated Man-machine Integration and design Analysis System (MIDAS) v5 model was extended to evaluate anticipated changes to flight deck and controller roles and responsibilities in NextGen approach and Land operations. Compared to conditions when the controllers are responsible for separation on decent to land phase of flight, the output from these model predictions suggest that the flight deck response time to detect the lead aircraft blunder will decrease, pilot scans to the navigation display will increase, and workload will increase.

Gore, Brian Francis; Hooey, Becky Lee; Mahlstedt, Eric; Foyle, David C.

2012-01-01

91

USDA Forest Service Gen. Tech. Rep. PSW-GTR-168. 1998. 71 Buffering the Buffer1  

E-print Network

USDA Forest Service Gen. Tech. Rep. PSW-GTR-168. 1998. 71 Buffering the Buffer1 Leslie M. Reid2 and Sue Hilton3 Abstract:Abstract:Abstract:Abstract:Abstract: Riparian buffer strips are a widely accepted in forested areas, but controversy persists over how wide a buffer strip is necessary. The physical integrity

Standiford, Richard B.

92

Curtuteria numenii nov. gen., nov. sp. aus Numenius Phaeopus (L.) (Trematoda, Echinostomatidae, Himasthlinae)  

Microsoft Academic Search

Es wird der Vertreter einer neuen Gattung beschrieben, Curtuteria numenii gen. nov., spec. nov., Trematoda, Echinostomatidae, Himasthlinae, aus dem Dünndarm von Numenius phaeopus (L.) von der Insel Hiddensee in der mittleren Ostsee. Von der Gattung Himasthla trennt ihn die Kürze des Uterus, ein deutlich abgegrenzter kleiner Prostatabezirk und die zahlreichen Divertikel der Exkretionshauptstämme im Vorderkörper, von Acanthoparyphium die Zahl der

L. Reimer

1963-01-01

93

Oswaldotrema nacinovici gen. nov. sp. nov. (Digenea: Philophthalmidae) from Numenius phaeopus (Aves: Scolopacidae) in Brazil.  

PubMed

A new genus, Oswaldotrema gen. nov. is proposed. Oswaldotrema nacinovici sp. nov. is descibed from Numenius phaeopus Latham, 1790. Differentiation from the other related genera, namely Philophthalmus, Pygorchis, Proctobium, Parorchis, Echinostephila, Cloacitrema, Pittacium, Ophthalmotrema, Skrjabinovermis and Paratrema, was based on morphological characters, mainly on those referring to the body surface, body shape, head, esophagus, pharynx, acetabulum, vitellaria, vitelline reservoir and seminal vesicle. PMID:10800187

Muniz-Pereira, L C; Pinto, R M

2000-01-01

94

Joostella marina gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the  

E-print Network

C for 24 h, according to the method described by Gerhardt et al. (1994). Catalase activity was investigated3). Hydrolysis of agar was tested on The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene

Bae, Jin-Woo

95

Elaphrobates euzeti gen. and sp. n. (Digenea: Sanguinicolidae) from Snappers (Lutjanidae) in the Gulf of Mexico  

Microsoft Academic Search

Elaphrobates euzeti gen. and sp. n. (Digenea: Sanguinicolidae) infects the heart and branchial vessels of the red snapper (Lutjanus campechanus) and the heart of the gray snapper (Lutjanus griseus) in the Gulf of Mexico. It has ventrolateral tegumental spine rows each consisting of 4-7 spines, an oral sucker with 6-7 concentric spine rows, sinuous posterior ceca extending to the ovary

Stephen A. Bullard; Robin M. Overstreet

2003-01-01

96

NASA/CR2012-217553 Safety Assurance in NextGen  

E-print Network

March 2012 NASA/CR­2012-217553 Safety Assurance in NextGen Cody Harrison Fleming, Melissa Spencer Aerospace Advanced Technology, Columbia, Maryland #12;NASA STI Program . . . in Profile Since its founding, NASA has been dedicated to the advancement of aeronautics and space science. The NASA scientific

Leveson, Nancy

97

CollegeofLiberalArtsandSciences Department of GenDer anD  

E-print Network

CollegeofLiberalArtsandSciences 208 Department of GenDer anD Women's stuDies 1208 University Hall, Barbara Ransby Director of Undergraduate Studies, Jennifer Brier Gender and Women's Studies of social roles filled by women and men across human cultures, and the place of sexuality in society

Illinois at Chicago, University of

98

GWAS in a Box: Statistical and Visual Analytics of Structured Associations via GenAMap  

PubMed Central

With the continuous improvement in genotyping and molecular phenotyping technology and the decreasing typing cost, it is expected that in a few years, more and more clinical studies of complex diseases will recruit thousands of individuals for pan-omic genetic association analyses. Hence, there is a great need for algorithms and software tools that could scale up to the whole omic level, integrate different omic data, leverage rich structure information, and be easily accessible to non-technical users. We present GenAMap, an interactive analytics software platform that 1) automates the execution of principled machine learning methods that detect genome- and phenome-wide associations among genotypes, gene expression data, and clinical or other macroscopic traits, and 2) provides new visualization tools specifically designed to aid in the exploration of association mapping results. Algorithmically, GenAMap is based on a new paradigm for GWAS and PheWAS analysis, termed structured association mapping, which leverages various structures in the omic data. We demonstrate the function of GenAMap via a case study of the Brem and Kruglyak yeast dataset, and then apply it on a comprehensive eQTL analysis of the NIH heterogeneous stock mice dataset and report some interesting findings. GenAMap is available from http://sailing.cs.cmu.edu/genamap. PMID:24905018

Xing, Eric P.; Curtis, Ross E.; Schoenherr, Georg; Lee, Seunghak; Yin, Junming; Puniyani, Kriti; Wu, Wei; Kinnaird, Peter

2014-01-01

99

USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 313 Marbled Murrelet Populations of Washington--  

E-print Network

USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 313 Marbled Murrelet Populations of Washington Eldridge, Bellingham, Washington 98225 Abstract: Marbled Murrelets occur in Puget Sound marine habitats. Such long-term information is unavailable for Marbled Murrelets along the Pacific Ocean coast of Washington

Standiford, Richard B.

100

GenVirtual: An Augmented Reality Musical Game for Cognitive and Motor Rehabilitation  

Microsoft Academic Search

Electronic games have been used to stimulate cognitive functions such as attention, concentration and memory. This paper presents GenVirtual, which is an augmented reality musical game and is proposed to help people with learning disabilities. The intention is to help the patient in the following skills: creativity, attention, memory (storage and retrieval), planning, concentration, ready-response, hearing and visual perception, and

Ana Grasielle Dionisio Correa; Gilda Aparecida de Assis; Marilena do Nascimento; Irene Ficheman; Roseli de Deus Lopes

2007-01-01

101

Age cohort analysis in adoption of mobile data services: gen Xers versus baby boomers  

Microsoft Academic Search

Purpose – This study aims to examine the differences in adoption of mobile data services between two age cohorts (gen Xers and baby boomers). Three elements in the extended Technology Acceptance Model – perceived usefulness, perceived ease of use, and perceived fun – were used to identify the differences in adoption of mobile data services for the two age cohorts.

Kiseol Yang; Laura D. Jolly

2008-01-01

102

Cryptometrion aestuescens gen. sp. nov. (Cryphonectriaceae) pathogenic to Eucalyptus in Indonesia  

E-print Network

Cryptometrion aestuescens gen. sp. nov. (Cryphonectriaceae) pathogenic to Eucalyptus in Indonesia M, Indonesia. C Corresponding author. Email: Marieka.Gryzenhout@fabi.up.ac.za Abstract. The recently described on Eucalyptus. A recent investigation of dying Eucalyptus grandis clonal hedges in northern Sumatra, Indonesia

103

Xylochloris irregularis gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel subaerial coccoid green alga  

E-print Network

green alga JIR I´ NEUSTUPA 1 *, MAREK ELIA´ S1 , PAVEL SKALOUD 1 , YVONNE NE MCOVA´ 1 AND LENKA irregularis gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel subaerial coccoid green alga. Phycologia 50: 57­66. DOI: 10.2216/08-64.1 The phylogenetic diversity of subaerial coccoid green algae remains

104

Haplotype Association Analysis of AGT Variants with Hypertension-Related Traits: The HyperGEN Study  

Microsoft Academic Search

Objective: Function of the renin-angiotensin system is important to human hypertension, but its genetic etiology remains elusive. We set out to examine a hypothesis that multiple genetic variants in the system act together in blood pressure regulation, via intermediate phenotypes such as blood pressure reactivity. Methods: A sample of 531 hypertensive cases and 417 controls was selected from the HyperGEN

C. Charles Gu; Yen-Pei C. Chang; Steven C. Hunt; Karen Schwander; Donna Arnett; Luc Djousse; Gerardo Heiss; Al Oberman; Jean-Marc Lalouel; Mike Province; Aravinda Chakravarti; D. C. Rao

2005-01-01

105

Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics  

PubMed Central

Next-gen sequencing technologies have revolutionized data collection in genetic studies and advanced genome biology to novel frontiers. However, to date, next-gen technologies have been used principally for whole genome sequencing and transcriptome sequencing. Yet many questions in population genetics and systematics rely on sequencing specific genes of known function or diversity levels. Here, we describe a targeted amplicon sequencing (TAS) approach capitalizing on next-gen capacity to sequence large numbers of targeted gene regions from a large number of samples. Our TAS approach is easily scalable, simple in execution, neither time-nor labor-intensive, relatively inexpensive, and can be applied to a broad diversity of organisms and/or genes. Our TAS approach includes a bioinformatic application, BarcodeCrucher, to take raw next-gen sequence reads and perform quality control checks and convert the data into FASTA format organized by gene and sample, ready for phylogenetic analyses. We demonstrate our approach by sequencing targeted genes of known phylogenetic utility to estimate a phylogeny for the Pancrustacea. We generated data from 44 taxa using 68 different 10-bp multiplexing identifiers. The overall quality of data produced was robust and was informative for phylogeny estimation. The potential for this method to produce copious amounts of data from a single 454 plate (e.g., 325 taxa for 24 loci) significantly reduces sequencing expenses incurred from traditional Sanger sequencing. We further discuss the advantages and disadvantages of this method, while offering suggestions to enhance the approach. PMID:22002916

Bybee, Seth M.; Bracken-Grissom, Heather; Haynes, Benjamin D.; Hermansen, Russell A.; Byers, Robert L.; Clement, Mark J.; Udall, Joshua A.; Wilcox, Edward R.; Crandall, Keith A.

2011-01-01

106

Leptochlorella corticola gen. et sp. nov. and Kalinella apyrenoidosa sp. nov.: two novel  

E-print Network

Leptochlorella corticola gen. et sp. nov. and Kalinella apyrenoidosa sp. nov.: two novel Chlorella algal genus, Chlorella, which accommodated coccoid unicellular green algal species with globular to oval. These algae share the general Chlorella-like morphology and their 18S rRNA and rbcL gene sequences place them

107

CottonGen: a genomics, genetics and breeding database for cotton research  

PubMed Central

CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, visualization and data retrieval of cotton research data. CottonGen contains annotated whole genome sequences, unigenes from expressed sequence tags (ESTs), markers, trait loci, genetic maps, genes, taxonomy, germplasm, publications and communication resources for the cotton community. Annotated whole genome sequences of Gossypium raimondii are available with aligned genetic markers and transcripts. These whole genome data can be accessed through genome pages, search tools and GBrowse, a popular genome browser. Most of the published cotton genetic maps can be viewed and compared using CMap, a comparative map viewer, and are searchable via map search tools. Search tools also exist for markers, quantitative trait loci (QTLs), germplasm, publications and trait evaluation data. CottonGen also provides online analysis tools such as NCBI BLAST and Batch BLAST. PMID:24203703

Yu, Jing; Jung, Sook; Cheng, Chun-Huai; Ficklin, Stephen P.; Lee, Taein; Zheng, Ping; Jones, Don; Percy, Richard G.; Main, Dorrie

2014-01-01

108

Adm. Greenert and Gen. Amos: A New Naval Era Publication: Proceedings Magazine  

E-print Network

Description: Adm. Greenert and Gen. James Amos discuss how the Navy-Marine Corps team will adapt, the importance of forward deployed units, the global influence of hospital ships, defending against piracy" which naval ships and aircraft carry or employ. CNO's Diversity Vision Publication: Navy Personnel

109

USDA Forest Service Gen. Tech. Rep. RMRS-GTR-176. 2006 55 Introduction_______________________  

E-print Network

USDA Forest Service Gen. Tech. Rep. RMRS-GTR-176. 2006 55 Introduction_______________________ Fire.Thevitalrolethatfireplaysincontrollingthe structure of an ecosystem underscores the need for us to increase our knowledge of past and current fire regimes (Morgan and others 1994). Dendrochronological recon- structions of fire histories provide

Swetnam, Thomas W.

110

Mol Gen Genet (1988)211:266-271 Springer-Verlag1988  

E-print Network

Mol Gen Genet (1988)211:266-271 © Springer-Verlag1988 Transformation with a mutant of achieving this is through the genetic transformation of plants to herbicide resistance. The prerequisites-mediated transformation the gene conferred a high level of herbicide resistance. These results suggest that the cloned

Haughn, George

111

Thaumamermis cosgrovei n. gen., n. sp. (Mermithidae: Nematoda) parasitizing terrestrial isopods (Isopoda: Oniscoidea)  

Microsoft Academic Search

Summary  A new mermithid nematode, Thaumamermis cosgrovei n. gen., n. sp. (Mermithidae: Nematoda) was found parasitizing two terrestrial isopods (Isopoda: Oniscoidea) in California. The hosts, Armadillidium vulgare (Latr.) (a pillbug) and Porcellio scaber (Latr.) (a sowbug) represent the first cases of isopods attacked by mermithid nematodes. The genus Thaumamermis can be distinguished from all previously described mermithids by the extremely dimorphic

George O. Poinar

1981-01-01

112

FDP-GEN Federal Demonstration Project (FDP) General Terms and Conditions  

NSF Publications Database

Title : FDP-GEN Federal Demonstration Project (FDP) General Terms and Conditions Type : Grant Conditions NSF Org: OD / LPA Date : January 7, 1994 File : fdpgen Federal Demonstration Project General Terms and Conditions Article Subject 1. Recipient Responsibilities and Federal Requirements . 5 17. Use of U.S.-Flag Air Carriers . 7 28. Research Involving Recombinant DNA Molecules.

113

Next-Gen Voting Systems for the 99% Philip B. Stark  

E-print Network

Next-Gen Voting Systems for the 99% Philip B. Stark Department of Statistics University of California, Berkeley EVN Annual Conference San Diego, CA 5­7 March 2014 #12;So you need a new voting system anything essential to cast votes on election day: Usability of equipment and ballots, reliability of BMDs

Stark, Philip B.

114

GenGIS 2: Geospatial Analysis of Traditional and Genetic Biodiversity, with New Gradient Algorithms and an Extensible Plugin Framework  

PubMed Central

GenGIS is free and open source software designed to integrate biodiversity data with a digital map and information about geography and habitat. While originally developed with microbial community analyses and phylogeography in mind, GenGIS has been applied to a wide range of datasets. A key feature of GenGIS is the ability to test geographic axes that can correspond to routes of migration or gradients that influence community similarity. Here we introduce GenGIS version 2, which extends the linear gradient tests introduced in the first version to allow comprehensive testing of all possible linear geographic axes. GenGIS v2 also includes a new plugin framework that supports the development and use of graphically driven analysis packages: initial plugins include implementations of linear regression and the Mantel test, calculations of alpha-diversity (e.g., Shannon Index) for all samples, and geographic visualizations of dissimilarity matrices. We have also implemented a recently published method for biomonitoring reference condition analysis (RCA), which compares observed species richness and diversity to predicted values to determine whether a given site has been impacted. The newest version of GenGIS supports vector data in addition to raster files. We demonstrate the new features of GenGIS by performing a full gradient analysis of an Australian kangaroo apple data set, by using plugins and embedded statistical commands to analyze human microbiome sample data, and by applying RCA to a set of samples from Atlantic Canada. GenGIS release versions, tutorials and documentation are freely available at http://kiwi.cs.dal.ca/GenGIS, and source code is available at https://github.com/beiko-lab/gengis. PMID:23922841

Parks, Donovan H.; Mankowski, Timothy; Zangooei, Somayyeh; Porter, Michael S.; Armanini, David G.; Baird, Donald J.; Langille, Morgan G. I.; Beiko, Robert G.

2013-01-01

115

Santa Fe Institute Working Paper 11-05-XXX arxiv.org:1105.XXXX [physics.gen-ph  

E-print Network

#12;Santa Fe Institute Working Paper 11-05-XXX arxiv.org:1105.XXXX [physics.gen-ph] Information at Merced, 5200 North Lake Road, Merced, CA 95343 3 Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM

116

Mercury: Next-gen Data Analysis and Annotation Pipeline (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)  

ScienceCinema

David Sexton (Baylor) gives a talk titled "Mercury: Next-gen Data Analysis and Annotation Pipeline" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

Sexton, David [Baylor

2013-01-25

117

Mercury: Next-gen Data Analysis and Annotation Pipeline (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)  

SciTech Connect

David Sexton (Baylor) gives a talk titled "Mercury: Next-gen Data Analysis and Annotation Pipeline" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

Sexton, David [Baylor

2012-06-01

118

Gen-Probe Rapid Diagnostic System for the Mycobacterium avium complex does not distinguish between Mycobacterium avium and Mycobacterium paratuberculosis.  

PubMed Central

Three reference and 16 field strains of Mycobacterium paratuberculosis were tested with the Gen-Probe Mycobacterium avium complex DNA probe (Gen-Probe Inc., San Diego, Calif.). All reference strains and 12 of 16 field strains gave positive hybridization results with the probe. This study shows that the M. avium complex probe does not distinguish between M. avium and M. paratuberculosis and indicates heterogeneity in the 16S rRNA gene of M. paratuberculosis. PMID:2037681

Thoresen, O F; Saxegaard, F

1991-01-01

119

Identification and Characterization of Key Human Performance Issues and Research in the Next Generation Air Transportation System (NextGen)  

NASA Technical Reports Server (NTRS)

This report identifies key human-performance-related issues associated with Next Generation Air Transportation System (NextGen) research in the NASA NextGen-Airspace Project. Four Research Focus Areas (RFAs) in the NextGen-Airspace Project - namely Separation Assurance (SA), Airspace Super Density Operations (ASDO), Traffic Flow Management (TFM), and Dynamic Airspace Configuration (DAC) - were examined closely. In the course of the research, it was determined that the identified human performance issues needed to be analyzed in the context of NextGen operations rather than through basic human factors research. The main gaps in human factors research in NextGen were found in the need for accurate identification of key human-systems related issues within the context of specific NextGen concepts and better design of the operational requirements for those concepts. By focusing on human-system related issues for individual concepts, key human performance issues for the four RFAs were identified and described in this report. In addition, mixed equipage airspace with components of two RFAs were characterized to illustrate potential human performance issues that arise from the integration of multiple concepts.

Lee, Paul U.; Sheridan, Tom; Poage, james L.; Martin, Lynne Hazel; Jobe, Kimberly K.

2010-01-01

120

PaGenBase: a pattern gene database for the global and dynamic understanding of gene function.  

PubMed

Pattern genes are a group of genes that have a modularized expression behavior under serial physiological conditions. The identification of pattern genes will provide a path toward a global and dynamic understanding of gene functions and their roles in particular biological processes or events, such as development and pathogenesis. In this study, we present PaGenBase, a novel repository for the collection of tissue- and time-specific pattern genes, including specific genes, selective genes, housekeeping genes and repressed genes. The PaGenBase database is now freely accessible at http://bioinf.xmu.edu.cn/PaGenBase/. In the current version (PaGenBase 1.0), the database contains 906,599 pattern genes derived from the literature or from data mining of more than 1,145,277 gene expression profiles in 1,062 distinct samples collected from 11 model organisms. Four statistical parameters were used to quantitatively evaluate the pattern genes. Moreover, three methods (quick search, advanced search and browse) were designed for rapid and customized data retrieval. The potential applications of PaGenBase are also briefly described. In summary, PaGenBase will serve as a resource for the global and dynamic understanding of gene function and will facilitate high-level investigations in a variety of fields, including the study of development, pathogenesis and novel drug discovery. PMID:24312499

Pan, Jian-Bo; Hu, Shi-Chang; Shi, Dan; Cai, Mei-Chun; Li, Yin-Bo; Zou, Quan; Ji, Zhi-Liang

2013-01-01

121

Towards Structuring Unstructured GenBank Metadata for Enhancing Comparative Biological Studies  

PubMed Central

Within large sequence repositories such as GenBank there is a wealth of metadata providing contextual information that may enhance search and retrieval of relevant sequences for a range of subsequent analyses. One challenge is the use of free-text in these metadata fields where approaches are needed to extract, structure, and encode essential information. The goal of the present study was to explore the feasibility of using a combination of existing resources for annotating unstructured GenBank metadata, initially focusing on the “host” and “isolation_source” fields. This paper summarizes early results for 10 host organisms that include a characterization of associated isolation sources with respect to biomedical ontologies and semantic types. The findings from this preliminary study provide insights to the rich amount of information captured within these unstructured metadata, guidance for addressing the challenges and issues encountered, and highlight the potential value for enriching comparative biological studies towards improving human health. PMID:22211174

Chen, Elizabeth S.; Sarkar, Indra Neil

2011-01-01

122

Development of an HPLC Method for the Quality Evaluation of ‘Ge-Gen-Qin-Lian’ Tablets Derived from Traditional Chinese Medicine  

Microsoft Academic Search

‘Ge-Gen-Qin-Lian’ tablets, made from three important medicinal plants (Radix Puerariae, Radix Scutellaria, and Rhizoma Coptidis), are derived from a traditional Chinese medicine named ‘Ge-Gen-Qin-Lian-Tang’. ‘Ge-Gen-Qin-Lian’ tablets are a widely used\\u000a botanical drug in China, and can be purchased at the counter. In this study, an HPLC method was developed for the quantification\\u000a of five important components (puerarin, berberine, baicalin, baicalein

H. B. Qu; Y. H. Ma; K. Yu; Y. Y. Cheng

2007-01-01

123

NextGen technologies for mid-term and far-term air traffic control operations  

Microsoft Academic Search

This paper describes technologies for mid-term and far-term air traffic control operations in the next generation air transportation system (NextGen). The technologies were developed and evaluated with human-in-the-loop simulations in the airspace operations laboratory (AOL) at the NASA Ames research center. The simulations were funded by several research focus areas within NASA's Airspace Systems program and some were co-funded by

Thomas Prevot

2009-01-01

124

PGMAP: A Privacy Guaranteed Mutual Authentication Protocol Conforming to EPC Class 1 Gen 2 Standards  

Microsoft Academic Search

To resolve the security vulnerabilities and comply with EPC class 1 Gen 2 UHF RFID (EPC C1G2) Standard at the same time, we present a privacy guaranteed mutual authentication protocol (PGMAP). By utilizing the existing functions and memory bank of tag, we amend the processing sequence based on current EPC architecture. An auto-updating index number IDS is enrolled to provide

Jiahao Wang; Edward C. Wong; Terry Ye

2008-01-01

125

Yamaguchia toyensis n. sp., n. gen. (Annelida, Clitellata, Lumbriculidae) from profundal lake habitat in Japan  

USGS Publications Warehouse

Yamaguchia toyensis n. sp., n. gen. is described from an oligotrophic caldera lake, Lake Toya, Hokkaido, Japan. Although the taxonomic affinities are unknown, the genus differs from all other Lumbriculidae in having the combination of testes and atria in X, a single, prosoporous male funnel per atrium, and spermathecae in XI. Unlike other Japanese lakes that have thus far been surveyed, Lake Toya supports abundant populations of lumbriculids in the profundal benthos.

Fend, S.V.; Ohtaka, A.

2004-01-01

126

Phylogenetic analysis of Alloiococcus otitis gen. nov., sp. nov., an organism from human middle ear fluid.  

PubMed

The partial 16S rRNA sequence of an unknown bacterium that was originally isolated from middle ear fluids of children with persistent otitis media was determined by reverse transcription. A comparison of this sequence with sequences from other gram-positive species having low guanine-plus-cytosine contents revealed that this bacterium represents a new line of descent, for which the name Alloiococcus otitis gen. nov., sp. nov., is proposed. The type strain is strain NCFB 2890. PMID:1371065

Aguirre, M; Collins, M D

1992-01-01

127

MicroGen: a MIAME compliant web system for microarray experiment information and workflow management  

PubMed Central

Background Improvements of bio-nano-technologies and biomolecular techniques have led to increasing production of high-throughput experimental data. Spotted cDNA microarray is one of the most diffuse technologies, used in single research laboratories and in biotechnology service facilities. Although they are routinely performed, spotted microarray experiments are complex procedures entailing several experimental steps and actors with different technical skills and roles. During an experiment, involved actors, who can also be located in a distance, need to access and share specific experiment information according to their roles. Furthermore, complete information describing all experimental steps must be orderly collected to allow subsequent correct interpretation of experimental results. Results We developed MicroGen, a web system for managing information and workflow in the production pipeline of spotted microarray experiments. It is constituted of a core multi-database system able to store all data completely characterizing different spotted microarray experiments according to the Minimum Information About Microarray Experiments (MIAME) standard, and of an intuitive and user-friendly web interface able to support the collaborative work required among multidisciplinary actors and roles involved in spotted microarray experiment production. MicroGen supports six types of user roles: the researcher who designs and requests the experiment, the spotting operator, the hybridisation operator, the image processing operator, the system administrator, and the generic public user who can access the unrestricted part of the system to get information about MicroGen services. Conclusion MicroGen represents a MIAME compliant information system that enables managing workflow and supporting collaborative work in spotted microarray experiment production. PMID:16351755

Burgarella, Sarah; Cattaneo, Dario; Pinciroli, Francesco; Masseroli, Marco

2005-01-01

128

Development of an Enhanced GenVARR™ (Generator Volt Ampere Reactive Reserve) System  

SciTech Connect

Transmission system operators require near real time knowledge of reactive power capability to reliably operate large electric power transmission systems. Reactive power produced by, or capable of being produced by, a power generator is often estimated based on a series of mega volt amperes (MVA) capability curves for the generator. These curves indicate the ability of the generator to produce real and reactive power under a variety of conditions. In transmission planning and operating studies, it is often assumed, based on estimates for these capability curves, that the generator can provide its rated MVA capability output when needed for system stability However, generators may not always operate at levels depicted by the maximum MVA capability curve due to present constraints. Transmission system operators utilizing the generators’ capability curves for operation decisions regarding transmission system stability or for planning horizons may overestimate the capability of the generators to supply reactive power when required. Southern Company has enhanced GenVARR(TM), the system of plant data query, retrieval, and analysis and calculates the actual – not estimated -- remaining reactive power output capability. The remaining reactive output is considered spinning reserve and is displayed graphically to transmission control center and generating plant operators to identify real time VAR limits. GenVARR is capable of aggregating generators from a defined region, or other user selectable combinations, to represent the available reserves that the operators are specifically interested in. GenVARR(TM) has been put into live production operation and is expected to significantly improve the overall visibility of the reactive reserve capability of the system. This new version of GenVARR(TM) significantly enhances the products structure and performance, and enables links to other key transmission system operation tools.

Schatz, Joe E.

2009-03-12

129

Complexity analysis of the Next Gen Air Traffic Management System: trajectory based operations.  

PubMed

According to Federal Aviation Administration traffic predictions currently our Air Traffic Management (ATM) system is operating at 150 percent capacity; forecasting that within the next two decades, the traffic with increase to a staggering 250 percent [17]. This will require a major redesign of our system. Today's ATM system is complex. It is designed to safely, economically, and efficiently provide air traffic services through the cost-effective provision of facilities and seamless services in collaboration with multiple agents however, contrary the vision, the system is loosely integrated and is suffering tremendously from antiquated equipment and saturated airways. The new Next Generation (Next Gen) ATM system is designed to transform the current system into an agile, robust and responsive set of operations that are designed to safely manage the growing needs of the projected increasingly complex, diverse set of air transportation system users and massive projected worldwide traffic rates. This new revolutionary technology-centric system is dynamically complex and is much more sophisticated than it's soon to be predecessor. ATM system failures could yield large scale catastrophic consequences as it is a safety critical system. This work will attempt to describe complexity and the complex nature of the NextGen ATM system and Trajectory Based Operational. Complex human factors interactions within Next Gen will be analyzed using a proposed dual experimental approach designed to identify hazards, gaps and elicit emergent hazards that would not be visible if conducted in isolation. Suggestions will be made along with a proposal for future human factors research in the TBO safety critical Next Gen environment. PMID:22317416

Lyons, Rhonda

2012-01-01

130

Reclassification of Cellulomonas cellulans (Stackebrandt and Keddie 1986) as Cellulosimicrobium cellulans gen. nov., comb. nov.  

PubMed

Phylogenetic analysis of 16S rDNA provides evidence that Cellulomonas cellulans branches outside the phylogenetic confines of the genus Cellulomonas. The distinct phylogenetic and chemotaxonomic status of Cellulomonas cellulans as a phylogenetic neighbour of the genus Promicromonospora, justifies the description of a new genus for which the name Cellulosimicrobium gen. nov. with the type species Cellulosimicrobium cellulans comb. nov. is proposed. PMID:11411667

Schumann, P; Weiss, N; Stackebrandt, E

2001-05-01

131

PubCrawler: keeping up comfortably with PubMed and GenBank  

Microsoft Academic Search

The free PubCrawler web service (http:\\/\\/www. pubcrawler.ie) has been operating for five years and sofarhasbroughtliteratureandsequenceupdatesto over 22000 users. It provides information on a perso- nalized web page whenever new articles appear in PubMed or when new sequences are found in GenBank that are specific to customized queries. The server also acts as an automatic alerting system by sending out short

Karsten Hokamp; Kenneth H. Wolfe

2004-01-01

132

Long-range correlation properties of coding and noncoding DNA sequences: GenBank analysis  

Microsoft Academic Search

An open question in computational molecular biology is whether long-range correlations are present in both coding and noncoding DNA or only in the latter. To answer this question, we consider all 33 301 coding and all 29 453 noncoding eukaryotic sequences-each of length larger than 512 base pairs (bp-in the present release of the GenBank to determine whether there is

S. V. Buldyrev; A. L. Goldberger; S. Havlin; R. N. Mantegna; M. E. Matsa; M. Simons; H. E. Stanley

1995-01-01

133

Initial Study of Controller\\/Automation Integration for NextGen Separation Assurance  

Microsoft Academic Search

This paper describes an initial human-in-the-loop part-task study on service provider- based automated separation assurance for the Next Generation Air Transportation System (NextGen). The study varied levels of trajectory-based separation assurance automation from manual trial planning to fully automated conflict resolution over 1x, 2x and 3x traffic densities. The experiment was conducted in the Airspace Operations Laboratory at NASA Ames

Thomas Prevot; Jeffrey Homola; Joey Mercer

2008-01-01

134

GrGen: A Fast SPO-Based Graph Rewriting Tool  

Microsoft Academic Search

WWW home page: http:\\/\\/www.info.uni-karlsruhe.de\\/~rubino Abstract. Graph rewriting is a powerful technique that requires graph pattern matching, which is an NP-complete problem. We present Gr- Gen, a generative programming system for graph rewriting, which ap- plies heuristic optimizations. According to Varro's benchmark it is at least one order of magnitude faster than any other tool known to us. Our graph rewriting

Rubino Geiß; Gernot Veit Batz; Daniel Grund; Sebastian Hack; Adam Szalkowski

2006-01-01

135

GOParGenPy: a high throughput method to generate Gene Ontology data matrices  

PubMed Central

Background Gene Ontology (GO) is a popular standard in the annotation of gene products and provides information related to genes across all species. The structure of GO is dynamic and is updated on a daily basis. However, the popular existing methods use outdated versions of GO. Moreover, these tools are slow to process large datasets consisting of more than 20,000 genes. Results We have developed GOParGenPy, a platform independent software tool to generate the binary data matrix showing the GO class membership, including parental classes, of a set of GO annotated genes. GOParGenPy is at least an order of magnitude faster than popular tools for Gene Ontology analysis and it can handle larger datasets than the existing tools. It can use any available version of the GO structure and allows the user to select the source of GO annotation. GO structure selection is critical for analysis, as we show that GO classes have rapid turnover between different GO structure releases. Conclusions GOParGenPy is an easy to use software tool which can generate sparse or full binary matrices from GO annotated gene sets. The obtained binary matrix can then be used with any analysis environment and with any analysis methods. PMID:23927037

2013-01-01

136

Enhanced and Synthetic Vision for Terminal Maneuvering Area NextGen Operations  

NASA Technical Reports Server (NTRS)

Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment with equivalent efficiency as visual operations. To meet this potential, research is needed for effective technology development and implementation of regulatory and design guidance to support introduction and use of SVS/EFVS advanced cockpit vision technologies in Next Generation Air Transportation System (NextGen) operations. A fixed-base pilot-in-the-loop simulation test was conducted at NASA Langley Research Center that evaluated the use of SVS/EFVS in NextGen low visibility ground (taxi) operations and approach/landing operations. Twelve crews flew approach and landing operations in a simulated NextGen Chicago O Hare environment. Various scenarios tested the potential for EFVS for operations in visibility as low as 1000 ft runway visibility range (RVR) and SVS to enable lower decision heights (DH) than can currently be flown today. Expanding the EFVS visual segment from DH to the runway in visibilities as low as 1000 RVR appears to be viable as touchdown performance was excellent without any workload penalties noted for the EFVS concept tested. A lower DH to 150 ft and/or possibly reduced visibility minima by virtue of SVS equipage appears to be viable when implemented on a Head-Up Display, but the landing data suggests further study for head-down implementations.

Kramer, Lynda J.; Bailey, Randall E.; Ellis, Kyle K. E.; Norman, R. Michael; Williams, Steven P.; Arthur, Jarvis J., III; Shelton, Kevin J.; Prinzel, Lawrence J., III

2011-01-01

137

Swedish Plectida (Nematoda). Part 6. Neocamacolaimus parasiticus gen. n., sp. n.  

PubMed

A new genus Neocamacolaimus gen. n., with one new species N. parasiticus gen. n., sp. n. is described from the benthic polychaete Sphaerosyllis cf. hystrix collected in the Skagerrak off the west coast of Sweden. Neocamacolaimus gen. n. is placed in the family Camacolaimidae and is particularly characterised by having annulated cuticle with lateral alae; setiform cephalic sensilla located at level with amphids; amphidial fovea ventrally spiral; buccal cavity without armament; pharynx muscular; nerve ring located at base of pharynx; male reproductive system diorchic with outstretched testes; spicules weakly arcuate with straight manubrium; gubernaculum absent; alveolar supplements located in the pharyngeal region; tubular supplements absent; tail conoid; caudal glands and spinneret present. Juveniles of this genus are particularly characterised by their parasitic lifestyle and the following unique morphological features: lips form a dorso-ventrally elongated perioral disc with internal sclerotizations: one midventral and two dorsosublateral (right and left); cephalic sensilla setiform, subventral sensilla are noticeably longer than the subdorsal ones; intestine extends posterior to rectum and anal opening, forming a post-anal pouch. PMID:24989765

Holovachov, Oleksandr; Boström, Sven

2014-01-01

138

Leptojacobus dorci n. gen., n. sp. (Nematoda: Diplogastridae), an Associate of Dorcus Stag Beetles (Coleoptera: Lucanidae)  

PubMed Central

A new species of diplogastrid nematode, Leptojacobus dorci n. gen., n. sp., was isolated from adults of the stag beetle Dorcus ritsemae (Coleoptera: Lucanidae) that were purchased from a pet shop in Japan. Leptojacobus n. gen. is circumscribed by a very thin, delicate body and by a small stoma with minute armature. A combination of other stomatal characters, namely the division of the cheilostom into adradial plates, the symmetry of the subventral stegostomatal sectors, and the presence of a thin, conical dorsal tooth, further distinguishes Leptojacobus n. gen. from other genera of Diplogastridae. Phylogenetic analysis of nearly full-length SSU rRNA sequences support the new species, together with an isolate identified previously as Koerneria luziae, to be excluded from a clade including all other molecularly characterized diplogastrids with teeth and stomatal dimorphism. Therefore, the new species will be of importance for reconstruction of ancestral character histories in Diplogastridae, a family circumscribed by a suite of feeding-related novelties. PMID:24644371

Kanzaki, Natsumi; Ragsdale, Erik J.; Susoy, Vladislav; Sommer, Ralf J.

2014-01-01

139

Defluviimonas denitrificans gen. nov., sp. nov., and Pararhodobacter aggregans gen. nov., sp. nov., non-phototrophic Rhodobacteraceae from the biofilter of a marine aquaculture.  

PubMed

Three Gram-negative bacterial strains were isolated from the biofilter of a recirculating marine aquaculture. They were non-pigmented rods, mesophiles, moderately halophilic, and showed chemo-organoheterotrophic growth on various sugars, fatty acids, and amino acids, with oxygen as electron acceptor; strains D9-3(T) and D11-58 were in addition able to denitrify. Phototrophic or fermentative growth could not be demonstrated. Phylogenetic analysis of the 16S rRNA gene sequences placed D9-3(T) and D11-58, and D1-19(T) on two distinct branches within the alpha-3 proteobacterial Rhodobacteraceae, affiliated with, but clearly separate from, the genera Rhodobacter, Rhodovulum, and Rhodobaca. Based on morphological, physiological, and 16S rRNA-based phylogenetic characteristics, the isolated strains are proposed as new species of two novel genera, Defluviimonas denitrificans gen. nov., sp. nov. (type strain D9-3(T)=DSM 18921(T)=ATCC BAA-1447(T); additional strain D11-58=DSM19039=ATCC BAA-1448) and Pararhodobacter aggregans gen. nov., sp. nov (type strain D1-19(T)=DSM 18938(T)=ATCC BAA-1446(T)). PMID:21959289

Foesel, Bärbel U; Drake, Harold L; Schramm, Andreas

2011-11-01

140

Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.  

PubMed Central

Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended. PMID:25157246

Breider, Sven; Scheuner, Carmen; Schumann, Peter; Fiebig, Anne; Petersen, Jorn; Pradella, Silke; Klenk, Hans-Peter; Brinkhoff, Thorsten; Goker, Markus

2014-01-01

141

Processing the loblolly pine PtGen2 cDNA microarray.  

PubMed

PtGen2 is a 26,496 feature cDNA microarray containing amplified loblolly pine ESTs. The array is produced in our laboratory for use by researchers studying gene expression in pine and other conifer species. PtGen2 was developed as a result of our gene discovery efforts in loblolly pine, and is comprised of sequences identified primarily from root tissues, but also from needle and stem. PtGen2 has been tested by hybridizing different Cy-dye labeled conifer target cDNAs, using both amplified and non-amplified indirect labeling methods, and also tested with a number of hybridization and washing conditions. This video focuses on the handling and processing of slides before and after pre-hybridization, as well as after hybridization, using some modifications to procedures developed previously. Also included, in text form only, are the protocols used for the generation, labeling and clean up of target cDNA s, as well as information on software used for downstream data processing. PtGen2 is printed with a proprietary print buffer that contains high concentrations of salt that can be difficult to remove completely. The slides are washed first in a warm SDS solution prior to pre-hybridization. After pre-hybridization, the slides are washed vigorously in several changes of water to complete removal of remaining salts. LifterSlips are then cleaned and positioned on the slides and labeled cDNA is carefully loaded onto the microarray by way of capillary action which provides for even distribution of the sample across the slide, and reduces the chance of bubble incorporation. Hybridization of targets to the array is done at 48 degrees C in high humidity conditions. After hybridization, a series of standard washes are done at 53 degrees C and room temperature for extended times. Processing PtGen2 slides using this technique reduces salt and SDS-derived artifacts often seen when the array is processed less rigorously. Hybridizing targets derived from several different conifer RNA sources, this processing protocol yielded fewer artifacts, reduced background, and provided better consistency among different experimental groups of arrays. PMID:19305380

Lorenz, W Walter; Yu, Yuan-Sheng; Simões, Marta; Dean, Jeffrey F D

2009-01-01

142

FutureGen: Stepping-Stone to Sustainable Fossil-Fuel Power Generation  

SciTech Connect

This presentation will highlight the U.S. Department of Energy's FutureGen Initiative. The nearly $1 billion government-industry project is a stepping-stone toward future coal-fired power plants that will produce hydrogen and electricity with zero-emissions, including carbon dioxide. The 275-megawatt FutureGen plant will initiate operations around 2012 and employ advanced coal gasification technology integrated with combined cycle electricity generation, hydrogen production, and carbon capture and sequestration. The initiative is a response to a presidential directive to develop a hydrogen economy by drawing upon the best scientific research to address the issue of global climate change. The FutureGen plant will be based on cutting-edge power generation technology as well as advanced carbon capture and sequestration systems. The centerpiece of the project will be coal gasification technology that can eliminate common air pollutants such as sulfur dioxide and nitrogen oxides and convert them to useable by-products. Gasification will convert coal into a highly enriched hydrogen gas, which can be burned much more cleanly than directly burning the coal itself. Alternatively, the hydrogen can be used in a fuel cell to produce ultra-clean electricity, or fed to a refinery to help upgrade petroleum products. Carbon sequestration will also be a key feature that will set the Futuregen plant apart from other electric power plant projects. The initial goal will be to capture 90 percent of the plant's carbon dioxide, but capture of nearly 100 percent may be possible with advanced technologies. Once captured, the carbon dioxide will be injected as a compressed fluid deep underground, perhaps into saline reservoirs. It could even be injected into oil or gas reservoirs, or into unmineable coal seams, to enhance petroleum or coalbed methane recovery. The ultimate goal for the FutureGen plant is to show how new technology can eliminate environmental concerns over the future use of coal--the most abundant fossil fuel in the United States with supplies projected to last 250 years. FutureGen's co-production of power and hydrogen will also serve as a stepping-stone to an environmentally sustainable energy future.

Zitney, S.E.

2006-11-01

143

Roles of SLX1-SLX4, MUS81-EME1, and GEN1 in avoiding genome instability and mitotic catastrophe.  

PubMed

The resolution of recombination intermediates containing Holliday junctions (HJs) is critical for genome maintenance and proper chromosome segregation. Three pathways for HJ processing exist in human cells and involve the following enzymes/complexes: BLM-TopoIII?-RMI1-RMI2 (BTR complex), SLX1-SLX4-MUS81-EME1 (SLX-MUS complex), and GEN1. Cycling cells preferentially use the BTR complex for the removal of double HJs in S phase, with SLX-MUS and GEN1 acting at temporally distinct phases of the cell cycle. Cells lacking SLX-MUS and GEN1 exhibit chromosome missegregation, micronucleus formation, and elevated levels of 53BP1-positive G1 nuclear bodies, suggesting that defects in chromosome segregation lead to the transmission of extensive DNA damage to daughter cells. In addition, however, we found that the effects of SLX4, MUS81, and GEN1 depletion extend beyond mitosis, since genome instability is observed throughout all phases of the cell cycle. This is exemplified in the form of impaired replication fork movement and S-phase progression, endogenous checkpoint activation, chromosome segmentation, and multinucleation. In contrast to SLX4, SLX1, the nuclease subunit of the SLX1-SLX4 structure-selective nuclease, plays no role in the replication-related phenotypes associated with SLX4/MUS81 and GEN1 depletion. These observations demonstrate that the SLX1-SLX4 nuclease and the SLX4 scaffold play divergent roles in the maintenance of genome integrity in human cells. PMID:24831703

Sarbajna, Shriparna; Davies, Derek; West, Stephen C

2014-05-15

144

Reclassification of rhizosphere bacteria including strains causing corky root of lettuce and proposal of Rhizorhapis suberifaciens gen. nov., comb. nov., Sphingobium mellinum sp. nov., Sphingobium xanthum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov.  

PubMed

The genus Rhizorhapis gen. nov. (to replace the illegitimate genus name Rhizomonas) is proposed for strains of Gram-negative bacteria causing corky root of lettuce, a widespread and important lettuce disease worldwide. Only one species of the genus Rhizomonas was described, Rhizomonas suberifaciens, which was subsequently reclassified as Sphingomonas suberifaciens based on 16S rRNA gene sequences and the presence of sphingoglycolipid in the cell envelope. However, the genus Sphingomonas is so diverse that further reclassification was deemed necessary. Twenty new Rhizorhapis gen. nov.- and Sphingomonas-like isolates were obtained from lettuce or sow thistle roots, or from soil using lettuce seedlings as bait. These and previously reported isolates were characterized in a polyphasic study including 16S rRNA gene sequencing, DNA-DNA hybridization, DNA G+C content, whole-cell fatty acid composition, morphology, substrate oxidation, temperature and pH sensitivity, and pathogenicity to lettuce. The isolates causing lettuce corky root belonged to the genera Rhizorhapis gen. nov., Sphingobium, Sphingopyxis and Rhizorhabdus gen. nov. More specifically, we propose to reclassify Rhizomonas suberifaciens as Rhizorhapis suberifaciens gen. nov., comb. nov. (type strain, CA1(T)?=?LMG 17323(T)?=?ATCC 49355(T)), and also propose the novel species Sphingobium xanthum sp. nov., Sphingobium mellinum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov. with the type strains NL9(T) (?=?LMG 12560(T)?=?ATCC 51296(T)), WI4(T) (?=?LMG 11032(T)?=?ATCC 51292(T)) and SP1(T) (?=?LMG 12581(T)?=?ATCC 51289(T)), respectively. Several strains isolated from lettuce roots belonged to the genus Sphingomonas, but none of them were pathogenic. PMID:24436067

Francis, Isolde M; Jochimsen, Kenneth N; De Vos, Paul; van Bruggen, Ariena H C

2014-04-01

145

New aerobic ammonium-dependent obligately oxalotrophic bacteria: description of Ammoniphilus oxalaticus gen. nov., sp. nov. and Ammoniphilus oxalivorans gen. nov., sp. nov.  

PubMed

The genus Ammoniphilus is proposed for aerobic endospore-forming Gram-variable rod-shaped bacteria, which are ammonium-dependent, obligately oxalotrophic and haloalkalitolerant, oxidase- and catalase-positive, mesophilic and motile by peritrichous flagella. Cell wall contained two electron-dense layers. The external layer consists of a chain of electron-dense granules morphologically resembling the cellulosomes of Clostridium thermocellum. Two species are described, Ammoniphilus oxalaticus gen. nov., sp. nov. and Ammoniphilus oxalivorans gen. nov., sp. nov. The type strains of these species are strains RAOx-1 (= DSM 11538) and RAOx-FS (= DSM 11537), respectively. Ammoniphilus strains were isolated from the rhizosphere of sorrel (Rumex acetosa) and from decaying wood. The strains require a high concentration of ammonium ions and use oxalate as the sole organic source of carbon and energy for growth; no growth factors were required. Growth occurred at pH 6.8-9.5. The optimum temperature and pH for growth were 28-30 degrees C and 8.0-8.5. All strains grew in a saturated solution of ammonium oxalate, and tolerated 3% NaCl. Whole-cell hydrolysates contain meso-diaminopimelic acid and glucose. The menaquinone of the strains was MK 7, and the major cellular fatty acids were 12-methyl tetradecanoic, cis-hexadec-9-enoic and hexadecanoic acids. The G + C content of the DNA was 45-46 mol% for A. oxalaticus and 42 mol% for A. oxalivorans. The almost complete 16S rDNA sequence of three strains of the two species of Ammoniphilus shows that the genus falls into the radiation of the Clostridium-Bacillus subphylum of Gram-positive bacteria. The closest phylogenetic neighbour of Ammoniphilus is Oxalophagus oxalicus. The DNA-DNA hybridization value between strains RAOx-1 and RAOx-FS was 39.7%. PMID:9542085

Zaitsev, G M; Tsitko, I V; Rainey, F A; Trotsenko, Y A; Uotila, J S; Stackebrandt, E; Salkinoja-Salonen, M S

1998-01-01

146

Enhanced Flight Vision Systems and Synthetic Vision Systems for NextGen Approach and Landing Operations  

NASA Technical Reports Server (NTRS)

Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment with equivalent efficiency as visual operations. To meet this potential, research is needed for effective technology development and implementation of regulatory standards and design guidance to support introduction and use of SVS/EFVS advanced cockpit vision technologies in Next Generation Air Transportation System (NextGen) operations. A fixed-base pilot-in-the-loop simulation test was conducted at NASA Langley Research Center that evaluated the use of SVS/EFVS in NextGen low visibility approach and landing operations. Twelve crews flew approach and landing operations in a simulated NextGen Chicago O'Hare environment. Various scenarios tested the potential for using EFVS to conduct approach, landing, and roll-out operations in visibility as low as 1000 feet runway visual range (RVR). Also, SVS was tested to evaluate the potential for lowering decision heights (DH) on certain instrument approach procedures below what can be flown today. Expanding the portion of the visual segment in which EFVS can be used in lieu of natural vision from 100 feet above the touchdown zone elevation to touchdown and rollout in visibilities as low as 1000 feet RVR appears to be viable as touchdown performance was acceptable without any apparent workload penalties. A lower DH of 150 feet and/or possibly reduced visibility minima using SVS appears to be viable when implemented on a Head-Up Display, but the landing data suggests further study for head-down implementations.

Kramer, Lynda J.; Bailey, Randall E.; Ellis, Kyle K. E.; Williams, Steven P.; Arthur, Jarvis J., III; Prinzel, Lawrence J., III; Shelton, Kevin J.

2013-01-01

147

High-resolution chromatography of nucleic acids on the Gen-Pak FAX column.  

PubMed

High-performance liquid chromatography (HPLC) on a Gen-Pak FAX column has been used to separate and purify microgram amounts of single- and double-stranded DNA and RNA molecules. HPLC of mixtures of DNA restriction fragments showed that fragments within the size range 0.125-23.1 kilobase were easily resolved. Supercoiled (form I) plasmid DNA molecules were readily separated from single-stranded circular DNA of the same length and from various DNA conformational isomers including nicked (form II) and linear (form III) species. Topological isomers generated from supercoiled plasmid DNA molecules by DNA topoisomerase I exhibited different retention times than supercoiled molecules. Supercoiled (form I) DNA molecules were resolved from fully relaxed (form IV) molecules. Synthetic oligonucleotides of 74 and 128 nucleotides in length were separated from failure sequences, as well as from other contaminating synthesis products. Single-stranded circular M13mp18 DNA molecules sufficiently pure for use in automated DNA sequencing systems were prepared by HPLC on a Gen-Pak FAX column. HPLC was also used to fractionate linear double-stranded porcine rotavirus genomic RNA fragments into size classes between 0.3 and 3 kilobase. Finally, HPLC of unfractionated Escherichia coli tRNA molecules resolved multiple species. In all cases, HPLC on Gen-Pak FAX was carried out in phosphate or Tris buffers at neutral pH in the presence of sodium chloride. Columns were not damaged by repeated exposure to impure samples, provided they were cleaned frequently with sodium hydroxide and acetic acid. Although procedures for resolution of the various size ranges for each class of DNA and RNA molecules require further optimization, our preliminary data on the separations obtained, the moderate salt concentrations employed, and the durability of the matrix suggest that this column merits further study. PMID:2462570

Stowers, D J; Keim, J M; Paul, P S; Lyoo, Y S; Merion, M; Benbow, R M

1988-07-01

148

Nuclear Data Needs Supporting Gen-IV Applications - INL Perspective and Initiatives  

SciTech Connect

Studies conducted in connection with the Department of Energy (DOE) Generation IV (Gen-IV) and Advanced Fuel Cycle (AFC) programs show that the transuranic nuclides can strongly influence the neutronic behavior of some advanced nuclear energy systems of interest. Essentially all integral nuclear parameters computed using modern reactor physics codes and data libraries are affected by propagation of uncertainty in the underlying nuclear data used in the computational models. These parameters include: Criticality (multiplication factor) Reactivity feedback coefficients (e.g., Doppler, Coolant Void) Kinetics parameters (e.g., Effective Delayed Neutron Fraction) Reactivity loss during irradiation (Burnup Swing) Peak power value Conversion ratio of sustainable cores Transmutation potential of burner cores Max dpa, maximum helium- and hydrogen-production, etc. Decay heat, radiotoxicity, and neutron and gamma radiation levels However, the necessary cross section information may be unavailable with the required accuracy from the current nuclear databases for some key nuclides of interest. As a specific example, recent sensitivity analyses for the Very High Temperature Gen-IV reactor concept (Taiwo et al, 2005a, Salvatores et al., 2005, Taiwo et al, 2005b), which features a somewhat harder thermal neutron spectrum and a significantly higher fuel burnup target than is the case for standard light-water reactors, show a potential need for improved cross sections for some isotopes, including 238U, 239Pu, 240Pu, 41Pu, and 243Am, primarily in the resonance energy range, in order to satisfy the defined accuracy requirements on key computed integral parameters. Other transuranic nuclides may be of similar importance for some of the other Gen-IV concepts, although the primary needs appear to be currently focused around a few plutonium and americium isotopes. The target accuracies identified in these studies are very stringent and will be a challenge to achieve in many cases. In this article we briefly review the conclusions and recommendations of recent international workshops on nuclear data needs for Gen-IV. Following this is a discussion of two specific activities undertaken by the Idaho National Laboratory (INL) to participate in the international effort to address these needs.

David W. Nigg

2005-07-01

149

Obesoconnus gen. n., a new bizarre Neotropical genus of Cyrtoscydmini (Coleoptera: Staphylinidae: Scydmaeninae).  

PubMed

A new Neotropical genus of Cyrtoscydmini, Obesoconnus gen. n., is described to accommodate two new species: O. guyanensis sp. n. (the type species of Obesoconnus) from French Guyana and O. mexicanus sp. n. from Mexico. The morphology of the new taxon is described and illustrated in detail, and its possible affinities to other Cyrtoscydmini are discussed. Despite external dissimilarities, the aedeagus of Obesoconnus highly resembles copulatory organs of Alloraphes and Parastenichnaphes; all these genera share the basal pumping apparatus and apically located ostium with asymmetrical apical projections. PMID:24870336

Ja?oszy?ski, Pawe?

2014-01-01

150

Electromagnetic Interactions GenERalized (EIGER): Applications at Johnson Space Center  

NASA Technical Reports Server (NTRS)

This slide presentation reviews the software framework for the analysis and design of complex electromagnetic systems. The system called Electromagnetic Interactions GenERalized (EIGER) is a hybrid finite element solution for wave equations and deru=ives boundary element solutions for integral equation formulations. Written in Fortran 90 Eiger uses object-oriented design methods to abstract key analysis components. EIGER has been applied to higher order modeling for analysis of antennas to assist in the design of the antennas of a mini-AERCam. EIGER might also be used to model the Ion Cyclotron Resonant heating stage for the VAriable Specific Impulse Magnetoplasma Rocket (VASIMR).

Dobbins, Justin A.; Fink, Patrick W.; Scully, Robert C.

2003-01-01

151

Competition between supercluster and stuffed cage structures in medium-sized Gen (n=30-39) clusters  

NASA Astrophysics Data System (ADS)

We have performed an unbiased global search for the geometries of low-lying Gen clusters in the size range of 30?n?39 using genetic algorithm incorporated with a tight-binding model. Density functional theory calculations were carried out to further optimize the isomer structures. Gen (n=30-39) clusters prefer the motif of supercluster structures stacked by several stable subunits such as Ge10 and Ge6, connecting via a few bridging atoms. Size-dependent cluster properties such as binding energy, HOMO-LUMO gaps, and ionization potentials were discussed and compared with experiments.

Wang, Lu; Zhao, Jijun

2008-01-01

152

Advanced Technology Development Program for Lithium-Ion Batteries: Gen 2 GDR Performance Evaluation Report  

SciTech Connect

The Advanced Technology Development Program has completed the performance evaluation of the second generation of lithium-ion cells (i.e., Gen 2 cells). This report documents the testing and analysis of the Gen 2 GDR cells, which were used to learn and debug the newly developed Technology Life Verification Test Manual. The purpose of the manual is to project a 15-year, 150,000 mile battery life capability with a 90% confidence interval using predictive models and short-term testing. The GDR cells were divided into two different matrices. The core-life test matrix consisted of calendar- and cycle-life cells with various changes to the four major acceleration factors (temperature, state-of-charge, throughput, and power rating). The supplemental-life test matrix consisted of cells subjected either to a path dependence study, or a comparison between the standard hybrid pulse power characterization test and the newly-developed minimum pulse power characterization test. Resistance and capacity results are reported.

Jon P. Christophersen; Chinh D. Ho; Gary L. Henriksen; David Howell

2006-07-01

153

Structural materials for Gen-IV nuclear reactors: Challenges and opportunities  

NASA Astrophysics Data System (ADS)

Generation-IV reactor design concepts envisioned thus far cater toward a common goal of providing safer, longer lasting, proliferation-resistant and economically viable nuclear power plants. The foremost consideration in the successful development and deployment of Gen-IV reactor systems is the performance and reliability issues involving structural materials for both in-core and out-of-core applications. The structural materials need to endure much higher temperatures, higher neutron doses and extremely corrosive environment, which are beyond the experience of the current nuclear power plants. Materials under active consideration for use in different reactor components include various ferritic/martensitic steels, austenitic stainless steels, nickel-base superalloys, ceramics, composites, etc. This paper presents a summary of various Gen-IV reactor concepts, with emphasis on the structural materials issues depending on the specific application areas. This paper also discusses the challenges involved in using the existing materials under both service and off-normal conditions. Tasks become increasingly complex due to the operation of various fundamental phenomena like radiation-induced segregation, radiation-enhanced diffusion, precipitation, interactions between impurity elements and radiation-produced defects, swelling, helium generation and so forth. Further, high temperature capability (e.g. creep properties) of these materials is a critical, performance-limiting factor. It is demonstrated that novel alloy and microstructural design approaches coupled with new materials processing and fabrication techniques may mitigate the challenges, and the optimum system performance may be achieved under much demanding conditions.

Murty, K. L.; Charit, I.

2008-12-01

154

Flight Deck Technologies to Enable NextGen Low Visibility Surface Operations  

NASA Technical Reports Server (NTRS)

Many key capabilities are being identified to enable Next Generation Air Transportation System (NextGen), including the concept of Equivalent Visual Operations (EVO) . replicating the capacity and safety of today.s visual flight rules (VFR) in all-weather conditions. NASA is striving to develop the technologies and knowledge to enable EVO and to extend EVO towards a Better-Than-Visual operational concept. This operational concept envisions an .equivalent visual. paradigm where an electronic means provides sufficient visual references of the external world and other required flight references on flight deck displays that enable Visual Flight Rules (VFR)-like operational tempos while maintaining and improving safety of VFR while using VFR-like procedures in all-weather conditions. The Langley Research Center (LaRC) has recently completed preliminary research on flight deck technologies for low visibility surface operations. The work assessed the potential of enhanced vision and airport moving map displays to achieve equivalent levels of safety and performance to existing low visibility operational requirements. The work has the potential to better enable NextGen by perhaps providing an operational credit for conducting safe low visibility surface operations by use of the flight deck technologies.

Prinzel, Lawrence (Lance) J., III; Arthur, Jarvis (Trey) J.; Kramer, Lynda J.; Norman, Robert M.; Bailey, Randall E.; Jones, Denise R.; Karwac, Jerry R., Jr.; Shelton, Kevin J.; Ellis, Kyle K. E.

2013-01-01

155

USDA Forest Service Gen. Tech. Rep. PSW-GTR-193. 2004. 207 The Future of Biodiversity in the Sierra Nevada  

E-print Network

USDA Forest Service Gen. Tech. Rep. PSW-GTR-193. 2004. 207 The Future of Biodiversity in the Sierra, recreation, air pollution, and climate change (Beesley 1996, Cahill and others 1996, Chang 1996, Duane 1996, Millar this volume). Our understanding of the individual effects of these stressors on subsets of biota

Standiford, Richard B.

156

Evaluation of Mixed-Mode Data-Link Communications for NextGen 4DT and Equivalent Visual Surface Operations  

NASA Technical Reports Server (NTRS)

By 2025, U.S. air traffic is predicted to increase 3-fold and may strain the current air traffic management system, which may not be able to accommodate this growth. In response to this challenge, a revolutionary new concept has been proposed for U.S. aviation operations, termed the Next Generation Air Transportation System or NextGen. Many key capabilities are being identified to enable NextGen, including the use of data-link communications. Because NextGen represents a radically different approach to air traffic management and requires a dramatic shift in the tasks, roles, and responsibilities for the flight deck, there are numerous research issues and challenges that must be overcome to ensure a safe, sustainable air transportation system. Flight deck display and crew-vehicle interaction concepts are being developed that proactively investigate and overcome potential technology and safety barriers that might otherwise constrain the full realization of NextGen. The paper describes simulation research examining data-link communications during 4DT and equivalent visual surface operations.

Prinzel, Lawrence J., III; Shelton, Kevin J.; Jones, Denise R.; Allamandola, Angela S.; Arthur, Jarvis, J., III; Bailey, Randall E.

2010-01-01

157

USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 219 Oceanographic Processes and Marine Productivity in Waters  

E-print Network

zones of enhanced primary production in which primary and secondary consumers may aggregate. In the moreUSDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 219 Oceanographic Processes and Marine central California to the Aleutian Islands. The offshore marine ecology of these waters is dominated

Standiford, Richard B.

158

USDA Forest Service Gen. Tech. Rep. PSW-GTR-203. 2007. 35 Fuels Planning: Science Synthesis and  

E-print Network

USDA Forest Service Gen. Tech. Rep. PSW-GTR-203. 2007. 35 Fuels Planning: Science Synthesis scientific information that can help guide their planning process. The Fuels Planning: Science Synthesis. To address this concern the Fuels Planning: Science Synthesis and Integration project was established

Standiford, Richard B.

159

Santa Fe Institute Working Paper 11-08-XXX arxiv.org:1108.XXXX [physics.gen-ph  

E-print Network

#12;Santa Fe Institute Working Paper 11-08-XXX arxiv.org:1108.XXXX [physics.gen-ph] How Hidden, University of California at Davis, One Shields Avenue, Davis, CA 95616 3 Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501 (Dated: August 5, 2011) We investigate a stationary process's crypticity

160

USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 535 Regional Patterns of Dead Wood in  

E-print Network

USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 535 Regional Patterns of Dead Wood regional patterns of variation in dead wood across 20 million ha of upland forests of all ownerships in Oregon and Washington, based on an analysis of data on snags and down wood collected on over 16,000 field

161

USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 71 Modeling the Delivery of Large Wood to  

E-print Network

USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 71 Modeling the Delivery of Large Wood forest structure and predict the delivery of wood to over 55 stream kilometers in a 28-square kilometer = 0.45). The model predicted that 83 percent of wood delivered to streams originated within 20 meters

Standiford, Richard B.

162

A Proactive Threshold Secret Sharing Scheme Handling Gen2 Privacy Threats Joaquin Garcia-Alfaro, Michel Barbeau, and Evangelos Kranakis  

E-print Network

because it requires spending more time at checkout stands and voids the benefits of the RFID technology offered to customers, such as processing of returns and automated recycling. Our goal is to provide lightweight enough to be deployed on low-cost Gen2 systems. The scheme protects EPC tag data against access

Barbeau, Michel

163

A Proactive Threshold Secret Sharing Scheme Handling Gen2 Privacy Threats Joaquin Garcia-Alfaro, Michel Barbeau, and Evangelos Kranakis  

E-print Network

from being effective because it requires spending more time at checkout stands and voids the benefits of the RFID technology offered to customers, such as processing of returns and automated recycling. Our goal cryptosystem lightweight enough to be deployed on low-cost Gen2 systems. The scheme protects EPC tag data

Garcia-Alfaro, Joaquin

164

Description of Bryantinus gen. n. from Sarawak, and New Distributional Records for Cerochusa cilioceps in Thailand (Coleoptera: Staphylinidae: Pselaphinae)  

PubMed Central

A new genus and species of the subtribe Batrisina from western Sarawak, Bryantinus matangus gen. et sp. n., is described, illustrated, and compared with related taxa. In addition, examination of a small series of batrisine material from Thailand revealed a new country record for Cerochusa cilioceps Yin & Nomura, which was previously known only from the island of Hainan in southern China. PMID:25409318

Yin, Zi-Wei; Li, Li-Zhen

2014-01-01

165

The Generic Spacecraft Analyst Assistant (GenSAA): A tool for automating spacecraft monitoring with expert systems  

NASA Technical Reports Server (NTRS)

Flight Operations Analysts (FOAs) in the Payload Operations Control Center (POCC) are responsible for monitoring a satellite's health and safety. As satellites become more complex and data rates increase, FOAs are quickly approaching a level of information saturation. The FOAs in the spacecraft control center for the COBE (Cosmic Background Explorer) satellite are currently using a fault isolation expert system named the Communications Link Expert Assistance Resource (CLEAR), to assist in isolating and correcting communications link faults. Due to the success of CLEAR and several other systems in the control center domain, many other monitoring and fault isolation expert systems will likely be developed to support control center operations during the early 1990s. To facilitate the development of these systems, a project was initiated to develop a domain specific tool, named the Generic Spacecraft Analyst Assistant (GenSAA). GenSAA will enable spacecraft analysts to easily build simple real-time expert systems that perform spacecraft monitoring and fault isolation functions. Lessons learned during the development of several expert systems at Goddard, thereby establishing the foundation of GenSAA's objectives and offering insights in how problems may be avoided in future project, are described. This is followed by a description of the capabilities, architecture, and usage of GenSAA along with a discussion of its application to future NASA missions.

Hughes, Peter M.; Luczak, Edward C.

1991-01-01

166

USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 257 Pollution and Fishing Threats to Marbled Murrelets  

E-print Network

the threat from these pollutants. Plastic ingestion does not appear to pose a serious threat to murreletsUSDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 257 Pollution and Fishing Threats to Marbled Murrelets D. Michael Fry1 Abstract: The principal pollutant threats to Marbled Murrelets are chlorinated

Standiford, Richard B.

167

USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 605 Demography of Snags in Eastside Pine  

E-print Network

USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 605 Demography of Snags in Eastside Pine, productivity, fire hazard, and human safety, all important components of ecosystem health. It is also useful Pacific Northwest Region, Medford, OR. #12;Snag Demography--Landram, Laudenslayer, and Atzet USDA Forest

Standiford, Richard B.

168

Rationale and Design of the National Registry of Genetically Triggered Thoracic Aortic Aneurysms and Cardiovascular Conditions (GenTAC) Registry  

PubMed Central

Background Although the management of thoracic aortic aneurysms (TAAs) has improved significantly, patients presenting with aortic dissections, rupture or other acute complications of TAAs continue to suffer high rates of morbidity and mortality. Accumulating data have indicated that many TAAs are due to underlying gene mutations. A comprehensive approach to the study of TAAs resulting from genetic mutations is needed to translate this information into advances in treatment. Objective The National Registry of Genetically Triggered Thoracic Aortic Aneurysms and Cardiovascular Conditions (GenTAC) was established to provide a biospecimen inventory and bioinformatics infrastructure to enable research to advance the clinical management of genetically-triggered TAAs and related complications. Methods The GenTAC Registry is a longitudinal observational cohort study enrolling patients with conditions related to genetically-induced TAAs from five regional clinical centers in the United States. Results Over 700 subjects with associated clinical histories, physical examinations, imaging data, and biospecimens have been enrolled in the Registry to date. Enrollment is expected to continue until September 2010. Total enrollment of nearly 3,000 subjects is expected. No interim analysis has yet been undertaken. Conclusions GenTAC has been established to facilitate studies by GenTAC investigators and others that will advance multiple scientific frontiers in thoracic aortic disease. Genotypic, proteomic, clinical, and imaging data will be integrated systematically with outcomes data to determine the optimal clinical management of patients suffering from genetically-induced TAAs. PMID:19185640

2010-01-01

169

USDA Forest Service Gen. Tech. Rep. PSW-GTR-193. 2004. 175 Invasive Exotic Plant Species in Sierra Nevada  

E-print Network

USDA Forest Service Gen. Tech. Rep. PSW-GTR-193. 2004. 175 Invasive Exotic Plant Species in Sierra/hcpd/species/t_e__spp/ann_te_rpt.shtml). Exotic plant species can directly compete with natives and cause their local displacement. In addition, and services of ecosystems. Potential impacts include alteration of disturbance regimes, changes in the food

Standiford, Richard B.

170

83USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Woody Root Biomass of 40-to 90-  

E-print Network

83USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Woody Root Biomass of 40- to 90- Year. Bledsoe2 Jerry Tecklin3 Abstract: This research examined biomass of blue oak (Quercus douglasii Hook root biomass outside the root ball. Root ball mass ranged from 7 to 184 kg, and estimated total root

Standiford, Richard B.

171

J. Phys. A: Math. Gen. 20 (1987) 1231-1238. Printed in the UK Kinetics of `cluster eating'  

E-print Network

J. Phys. A: Math. Gen. 20 (1987) 1231-1238. Printed in the UK Kinetics of `cluster eating' S Redner, D Ben-Avraham and B Kahng Center for Polymer Studies and Department of Physics, Boston University, Boston, MA 02215, USA Received 8 May 1986 Abstract. We introduce and study the kinetics of `cluster

Redner, Sidney

172

USDA Forest Service Gen.Tech. Rep. PSW-GTR-187. 2003. 17 II. The San Diego Association of  

E-print Network

USDA Forest Service Gen.Tech. Rep. PSW-GTR-187. 2003. 17 II. The San Diego Association to the south, and mountains and critical habitat to the east (fig. 3). San Diego County is faced with numerous, and the disappearance of open space are not unique to San Diego, but are also occurring in other regions of the state

Standiford, Richard B.

173

Transfer of Rhizobium loti, Rhizobium huakuii, Rhizobium mediterraneum, and Rhizobium to Mesorhizobium gen. nov. Rhizobium ciceri, tianshanense  

Microsoft Academic Search

Reasons are advanced for removal of Rhizobium ciceri, Rhizobium huakuii, Rhizobium loti, Rhizobium medi- terraneum, and Rhizobium tianshanense from the genus Rhizobium and for establishment of Mesorhizobium gen. nov. for these species. A description of the genus Mesorhizobium and amended descriptions of Mesorhizobium ciceri, Mesorhizobium huakuii, Mesorhizobium loti, Mesorhizobium mediterraneum, and Mezorhizobium tian- shanense are provided. In a review of

B. D. W. JARVIS; P. VAN BERKUM; W. X. CHEN; S. M. NOUR; M. P. FERNANDEZ; J. C. CLEYET-MAREL; M. GILLIS

174

PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees  

Microsoft Academic Search

Motivation: Seq-Gen is a program that will simulate the evolution of nucleotide sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. Nucleotide frequencies and other parameters of the model may be given and site-specific rate heterogeneity can also be incorporated in a number of

Andrew Rambaut; J. Adachi

1997-01-01

175

YouGenMap: a web platform for dynamic multi-comparative mapping and visualization of genetic maps.  

PubMed

Comparative genetic maps are used in examination of genome organization, detection of conserved gene order, and exploration of marker order variations. YouGenMap is an open-source web tool that offers dynamic comparative mapping capability of users' own genetic mapping between 2 or more map sets. Users' genetic map data and optional gene annotations are uploaded, either publically or privately, as long as they follow our template which is available in several standard file formats. Data is parsed and loaded into MySQL relational database to be displayed and compared against users' genetic maps or other public data available on YouGenMap. With the highly interactive GUIs, all public data on YouGenMap are maps available for visualization, comparison, search, filtration and download. YouGenMap web tool is available on the website (http://conifergdb.miamioh.edu/yougenmap) with the source-code repository at (http://sourceforge.net/projects/yougenmap/?source=directory). PMID:25009553

Batesole, Keith; Wimalanathan, Kokulapalan; Liu, Lin; Zhang, Fan; Echt, Craig S; Liang, Chun

2014-01-01

176

JENUFA GEN. NOV.: A NEW GENUS OF COCCOID GREEN ALGAE (CHLOROPHYCEAE, INCERTAE SEDIS) PREVIOUSLY RECORDED BY ENVIRONMENTAL SEQUENCING1  

E-print Network

JENUFA GEN. NOV.: A NEW GENUS OF COCCOID GREEN ALGAE (CHLOROPHYCEAE, INCERTAE SEDIS) PREVIOUSLY of unicellular green algae from algal biofilms growing on tree bark in a Southeast Asian tropical rainforest: AU, approximately unbiased; BBM, Bold basal medium; CAUP, Culture Collection of algae at Charles

177

Plant MetGenMAP: An Integrative Analysis System for Plant Systems Biology1[W][OA  

PubMed Central

The information and resources generated from diverse “omics” technologies provide opportunities for producing novel biological knowledge. It is essential to integrate various kinds of biological information and large-scale omics data sets through systematic analysis in order to describe and understand complex biological phenomena. For this purpose, we have developed a Web-based system, Plant MetGenMAP, which can comprehensively integrate and analyze large-scale gene expression and metabolite profile data sets along with diverse biological information. Using this system, significantly altered biochemical pathways and biological processes under given conditions can be retrieved rapidly and efficiently, and transcriptional events and/or metabolic changes in a pathway can be easily visualized. In addition, the system provides a unique function that can identify candidate promoter motifs associated with the regulation of specific biochemical pathways. We demonstrate the functions and application of the system using data sets from Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum), respectively. The results obtained by Plant MetGenMAP can aid in a better understanding of the mechanisms that underlie interesting biological phenomena and provide novel insights into the biochemical changes associated with them at the gene and metabolite levels. Plant MetGenMAP is freely available at http://bioinfo.bti.cornell.edu/tool/MetGenMAP. PMID:19819981

Joung, Je-Gun; Corbett, Anthony M.; Fellman, Shanna Moore; Tieman, Denise M.; Klee, Harry J.; Giovannoni, James J.; Fei, Zhangjun

2009-01-01

178

Ferganasaurus verzilini, gen. et sp. nov., a new neosauropod (Dinosauria, Saurischia, Sauropoda) from the Middle Jurassic of Fergana Valley, Kirghizia  

Microsoft Academic Search

A partial sauropod skeleton from the Middle Jurassic (Callovian) Balabansai Formation in Kirghizia, comprising two dorsal and 16 caudal vertebrae, pelvis and limb bones is described and referred to Ferganasaurus verzilini, gen. et sp. nov. The manus is known only from drawings as original material has been lost; foot bones, except the astragalus, are unknown. Ferganasaurus forms an unresolved polytomy

Vladimir R. Alifanov; Alexander O. Averianov

2003-01-01

179

Molecular and ultrastructural characterization of Andreanna caspii n. gen., n. sp. (Microsporida: Amblyosporidae), a parasite of Ochlerotatus caspius (Diptera: Culicidae)  

Microsoft Academic Search

A new genus and species of microsporidia, Andreanna caspii n. gen., n. sp. is described from the mosquito, Ochlerotatus caspius (Pallas) based on ultrastructural morphology, developmental characteristics, and comparative sequence analyses of the small subunit (SSU) ribosomal DNA (rDNA). Parasite development is confined to fat body tissue and infected larvae appear swollen with dull white masses within the thorax and

Anastasia V. Simakova; Charles R. Vossbrinck; Theodore G. Andreadis

2008-01-01

180

313USDA Forest Service Gen.Tech. Rep. PSW-GTR-160. 1997. Effects of Livestock Grazing on Blue  

E-print Network

313USDA Forest Service Gen.Tech. Rep. PSW-GTR-160. 1997. Effects of Livestock Grazing on Blue Oak systems of livestock grazing and no grazing on the growth of blue oak (Quercus douglasii H. & A.) saplings were examined over a 4-year period in western Colusa County, California. In grazed plots, base

Standiford, Richard B.

181

327USDA Forest Service Gen.Tech. Rep. PSW-GTR-160. 1997. The Influence of Cattle Grazing on  

E-print Network

327USDA Forest Service Gen.Tech. Rep. PSW-GTR-160. 1997. The Influence of Cattle Grazing California ground squirrel (Spermophilus beecheyi) activity on replicated grazed and ungrazed pastures as the number of active burrows, generally declined in grazed and ungrazed pastures without oak canopy. Squirrel

Standiford, Richard B.

182

The gondwanan acritarch Bimerga bensonii gen. et sp. nov.: Paleogeographic and biostratigraphic importance in the Devonian malvinokaffric realm  

Microsoft Academic Search

The acritarch (organic?walled microphytoplankton) Bimerga bensonii gen. et sp. nov. has an elongate, bilaterally symmetrical vesicle with the poles bisected into two broad?based processes possessing homomorphic or heteromorphic terminations. This acritarch was first illustrated, and named in open nomenclature, from the subsurface of Ghana and is reported here from an outcrop sample of the Devonian Los Monos Formation and subsurface

Gordon D. Wood

1995-01-01

183

65USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Soil Characteristics of Blue Oak and  

E-print Network

65USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Soil Characteristics of Blue Oak and Coast, California, soils associated with blue oaks (Quercus douglasii) are slightly more acidic, have finer textures are richer in organic matter than those associated with blue oaks. Blue oaks seem to grow more frequently

Standiford, Richard B.

184

Similascarophis n. gen. n. spp. (Nematoda: Cystidicolidae) parasitizing marine fishes off the Chilean coast.  

PubMed

Similascarophis (Cystidicolidae) n. gen. is proposed. In the mouth of specimens of this genus, submedial labia are absent and pseudolabia do not have any part projecting toward the central oral opening. These nematodes were obtained from the alimentary tract of 7 marine fish species along the coast of Chile: Bovichthys chilensis Regan, Eleginops maclovinus (Cuvier), Pinguipes chilensis (Valenciennes), Cilus gilberti (Abbott), Cheilodactylus variegatus Valenciennes, Girella laevifrons (Tschudi), and Graus nigra Philippi. Morphology and morphometry are compared between 2 new Similascarophis species: Similascarophis maulensis n. sp. and S. chilensis n. sp., which differ in the presence of sublabia and in the length of the glandular esophagus and left spicule. We also recorded Similascarophis sp. in 2 other host species, which showed some distinct proportional measurements, although these differences were not sufficiently clear to identify them as a new species. PMID:15357077

Muñoz, Gabriela; González, María Teresa; George-Nascimento, Mario

2004-08-01

185

Enhanced vision for all-weather operations under NextGen  

NASA Astrophysics Data System (ADS)

Recent research in Synthetic/Enhanced Vision technology is analyzed with respect to existing Category II/III performance and certification guidance. The goal is to start the development of performance-based vision systems technology requirements to support future all-weather operations and the NextGen goal of Equivalent Visual Operations. This work shows that existing criteria to operate in Category III weather and visibility are not directly applicable since, unlike today, the primary reference for maneuvering the airplane is based on what the pilot sees visually through the "vision system." New criteria are consequently needed. Several possible criteria are discussed, but more importantly, the factors associated with landing system performance using automatic and manual landings are delineated.

Bailey, Randall E.; Kramer, Lynda J.; Williams, Steven P.

2010-04-01

186

The haemosporidian parasites of bats with description of Sprattiella alecto gen. nov., sp. nov.  

PubMed Central

Four species of Haemoproteidae were found in Pteropus alecto Temminck, 1837 in Queensland, Australia: i) Johnsprentia copemani, Landau et al., 2012; ii) Sprattiella alecto gen. nov., sp. nov., characterised by schizonts in the renal vessels; iii) Hepatocystis levinei, Landau et al., 1985, originally described from Pteropus poliocephalus Temminck, 1825 and, experimentally from Culicoides nubeculosus and found in this new host and for which features of the hepatic schizonts are reported; iv) gametocytes of Hepatocystis sp. which are illustrated but cannot be assigned to a known species. A tentative interpretation of phylogenetic characters of haemosporidians of bats is provided from the morphology of the gametocytes and localisation of the tissue stages with respect to recent data on the phylogeny of bats. PMID:22550624

Landau, I.; Chavatte, J.M.; Karadjian, G.; Chabaud, A.; Beveridge, I.

2012-01-01

187

Microstructure stability of candidate stainless steels for Gen-IV SCWR fuel cladding application  

NASA Astrophysics Data System (ADS)

In the past few years, significant progress has been made in materials selection for Gen-IV SCWR fuel cladding applications. Current studies indicate that austenite stainless steels such as 310H are promising candidates for in-core applications. Alloys in this group are promising for their corrosion resistance, SCC resistance, high temperature mechanical properties and creep resistance at temperatures up to 700 °C. However, one under-studied area of this alloy is the long-term microstructure stability under the proposed reactor operating condition. Unstable microstructure not only results in embrittlement but also has the potential to reduce their resistance to corrosion or stress-corrosion cracking. In this study, stainless steels 310H and 304H were tested for their SCWR corrosion resistance and microstructure stability.

Li, Jian; Zheng, W.; Penttilä, S.; Liu, P.; Woo, O. T.; Guzonas, D.

2014-11-01

188

Development of Distributed Generic Simulator (GenSim) through Invention of Simulated Network (simNetwork)  

NASA Astrophysics Data System (ADS)

A simulated network protocol provides the capability of distributed simulation to a generic simulator. Through this, full coverage of management of data and service handling among separated simulators is achieved. The distributed simulation environment is much more conducive to handling simulation load balancing and hazard treatment than a standalone computer. According to the simulated network protocol, one simulator takes on the role of server and the other simulators take on the role of client, and client is controlled by server. The purpose of the simulated network protocol is to seamlessly connect multiple simulator instances into a single simulation environment. This paper presents the development of a simulated network (simNetwork) that provides the capability of distributed simulation to a generic simulator (GenSim), which is a software simulator of satellites that has been developed by the Korea Aerospace Research Institute since 2010, to use as a flight software! validation bench for future satellite development.

Koo, Cheol-Hea; Lee, Hoon-Hee; Cheon, Yee-Jin

2011-09-01

189

Turicibacter sanguinis gen. nov., sp. nov., a novel anaerobic, Gram-positive bacterium.  

PubMed

An unknown, strictly anaerobic, Gram-positive, rod-shaped bacterium (strain MOL361T) was isolated from a blood culture of a febrile patient with acute appendicitis and characterized using phenotypic and molecular methods. Fatty acid analysis and biochemical examination indicated that the isolate most closely resembles members of the Gram-positive bacteria with low DNA G+C content. 16S rDNA sequencing revealed a relatively high overall similarity (97%) to an uncultured bacterium, but these two strains both exhibit low (<87%) 16S rDNA similarity to other bacteria. Phylogenetic analysis with different treeing methods showed that this strain forms a novel line of descent within the Gram-positive bacteria with low G+C content. Strain MOL361T is described as the type strain of a novel species within a new genus, Turicibacter sanguinis gen. nov., sp. nov. PMID:12148638

Bosshard, Philipp P; Zbinden, Reinhard; Altwegg, Martin

2002-07-01

190

Halogeometricum borinquense gen. nov., sp. nov., a novel halophilic archaeon from Puerto Rico.  

PubMed

A novel extremely halophilic archaeon was isolated from the solar salterns of Cabo Rojo, Puerto Rico. The organism is very pleomorphic, motile and requires at least 8% (w/v) NaCl to grow. Polar lipid composition revealed the presence of a novel non-sulfate-containing glycolipid and the absence of the glycerol diether analogue of phosphatidylglycerosulfate. The G + C content of the DNA is 59 mol%. On the basis of 16S rRNA sequence data, the new isolate cannot be classified in one of the recognized genera, but occupies a position that is distantly related to the genus Haloferax. All these features justify the creation of a new genus and a new species for the family Halobacteriaceae, order Halobacteriales. The name Halogeometricum borinquense gen. nov., sp. nov. is proposed. The type strain is ATCC 700274T. PMID:9828431

Montalvo-Rodríguez, R; Vreeland, R H; Oren, A; Kessel, M; Betancourt, C; López-Garriga, J

1998-10-01

191

NASA System-Level Design, Analysis and Simulation Tools Research on NextGen  

NASA Technical Reports Server (NTRS)

A review of the research accomplished in 2009 in the System-Level Design, Analysis and Simulation Tools (SLDAST) of the NASA's Airspace Systems Program is presented. This research thrust focuses on the integrated system-level assessment of component level innovations, concepts and technologies of the Next Generation Air Traffic System (NextGen) under research in the ASP program to enable the development of revolutionary improvements and modernization of the National Airspace System. The review includes the accomplishments on baseline research and the advancements on design studies and system-level assessment, including the cluster analysis as an annualization standard of the air traffic in the U.S. National Airspace, and the ACES-Air MIDAS integration for human-in-the-loop analyzes within the NAS air traffic simulation.

Bardina, Jorge

2011-01-01

192

Tucunarella n. Gen. and other dactylogyrids (Monogenoidea) from cichlid fish (Perciformes) from Peruvian Amazonia.  

PubMed

During parasitological research on cichlid fish from the tributaries of the Amazon River around Iquitos, Peru, the following gill monogenoidean species were found: Tucunarella cichlae n. gen. and n. sp. from Cichla monoculus Spix and Agassiz; Gussevia alioides Kritsky, Thatcher, and Boeger, 1986 from Heros severus Heckel; Gussevia asota Kritsky, Thatcher, and Boeger, 1989 from Astronotus ocellatus (Agassiz); Gussevia disparoides Kritsky, Thatcher, and Boeger, 1986 from H. severus (all new geographical records) and Cichlasoma amazonarum Kullander (new host record); Gussevia longihaptor (Mizelle and Kritsky, 1969) Kritsky, Thatcher, and Boeger, 1986 and Gussevia undulata Kritsky, Thatcher, and Boeger, 1986 from C. monoculus ; Sciadicleithrum satanopercae Yamada, Takemoto, Bellay, and Pavanelli, 2008 from Satanoperca jurupari Heckel; and Sciadicleithrum variabilum (Mizelle and Kritsky, 1969) Kritsky, Thatcher, and Boeger, 1989 from C. amazonarum (new host and geographical records). Tucunarella n. gen. is proposed to accommodate a new species, Tucunarella cichlae , which is its type and only known species in the genus. The new genus is characterized by, besides a very large body size (about 1.5 mm vs. much less than 1 mm in other ancyrocephaline genera in Amazonia), a thickened tegument, 1 pair of eyes, overlapping gonads (testis dorsal to the germarium), nonarticulated male copulatory organ (MCO) and accessory piece, a coiled (counterclockwise) MCO, a dextral vaginal aperture, a haptor armed with 2 pairs of anchors (each with broad base and subequal roots, which are marginally folded), and dorsal and ventral bars and 14 hooks with protruding blunt thumbs and 2 different shapes (slender vs. slightly expanded shanks). Illustrations and data on morphological and biometric variability of individual species from different hosts are provided. The present data provide evidence of a relatively wide host specificity of gill monogenoideans parasitic in South American cichlids. PMID:20557192

Mendoza-Franco, Edgar F; Scholz, T; Rozkosná, P

2010-06-01

193

Evaluation of the GenBank, EzTaxon, and BIBI Services for Molecular Identification of Clinical Blood Culture Isolates That Were Unidentifiable or Misidentified by Conventional Methods  

PubMed Central

We compared the 16S rRNA gene sequencing results analyzed with the GenBank, EzTaxon, and BIBI databases for blood culture specimens for which identifications were incomplete, conflicting, or unidentifiable using conventional methods. Analyses performed using GenBank combined with EzTaxon (kappa = 0.79) were more discriminative than those using other databases alone or in combination with a second database. PMID:22403421

Park, Kyung Sun; Ki, Chang-Seok; Kang, Cheol-In; Kim, Yae-Jean; Chung, Doo Ryeon; Peck, Kyong Ran; Song, Jae-Hoon

2012-01-01

194

The Caenorhabditis elegans Homolog of Gen1\\/Yen1 Resolvases Links DNA Damage Signaling to DNA Double-Strand Break Repair  

Microsoft Academic Search

DNA double-strand breaks (DSBs) can be repaired by homologous recombination (HR), which can involve Holliday junction (HJ) intermediates that are ultimately resolved by nucleolytic enzymes. An N-terminal fragment of human GEN1 has recently been shown to act as a Holliday junction resolvase, but little is known about the role of GEN-1 in vivo. Holliday junction resolution signifies the completion of

Aymeric P. Bailly; Alasdair Freeman; Julie Hall; Anne-Cécile Déclais; Arno Alpi; David M. J. Lilley; Shawn Ahmed; Anton Gartner

2010-01-01

195

GenBank at Los Alamos: User manual, training guide, and reference manual for the ASCII AWB  

SciTech Connect

The GenBank project at Los Alamos collects nucleotide sequence submissions from the biological research community. This work includes the processing of data received in several different forms as well as maintenance and quality control on those submissions. This manual explains the procedures involved in that work for both Los Alamos GenBank staff and off-site users. The GenBank database stores annotated DNA sequences. This manual contains the procedures for depositing these sequences into the database. There are two ways to do this. Either the sequence arrives at GenBank as a submission and is entered by the database staff or the sequence is directly entered by an off-site user. The Annotator's WorkBench (AWB), which is a database browsing and editing tool, is used in both cases. This manual is for GenBank staff and off-site users of the GenBank database at the Los Alamos National Laboratory. It contains an introduction and tutorials for AWB, as well as procedures for entering sequences either as submissions or as data directly deposited by an off-site user. Instructions for all of these are found in Chapters 2 through 4. The introduction to AWB is in Chapter 2. Instructions for submission handling are in Chapter 3. Instructions for entering sequence information are in Chapter 4. Off-site users should look at section 4.3 for instructions on entering a sequence. In addition, the manual describes various in-house curatorial tasks that are part of maintaining the database, as well as the procedures and conventions for annotating sequences. The procedures for annotation and review are in Chapters 5 and 6. The description of in-house curator's tasks is in Chapter 7. The appendices contain: Annotation conventions, two reference chapters on AWB and other utility programs, a complete list of all the forms, fields, and commands in AWB and descriptions of other (non-AWB) software utilities used by database staff.

Reese, G.C.; Keen, G.M.; Gilna, P.; Cinkosky, M.J.

1993-03-15

196

Next-Gen Sequencing-Based Mapping and Identification of Ethyl Methanesulfonate-Induced Mutations in Arabidopsis thaliana.  

PubMed

Forward genetic analysis using ethyl methanesulfonate (EMS) mutagenesis has proven to be a powerful tool in biological research, but identification and cloning of causal mutations by conventional genetic mapping approaches is a painstaking process. Recent advances in next-gen sequencing have greatly invigorated the process of identifying EMS-induced mutations corresponding to a specific phenotype in model genetic hosts, including the plant Arabidopsis thaliana and the nematode Caenorhabditis elegans. Next-gen sequencing of bulked F2 mutant recombinants produces a wealth of high-resolution genetic data, provides enhanced delimitation of the genomic location of mutations, and greatly reduces hands-on time while maintaining high accuracy and reproducibility. In this unit, a detailed procedure to simultaneously map and identify EMS mutations in Arabidopsis is described. Curr. Protoc. Mol. Biol. 108:7.18.1-7.18.16. © 2014 by John Wiley & Sons, Inc. PMID:25271717

Zhang, Xue-Cheng; Millet, Yves; Ausubel, Frederick M; Borowsky, Mark

2014-01-01

197

Schlegelella thermodepolymerans gen. nov., sp. nov., a novel thermophilic bacterium that degrades poly(3-hydroxybutyrate-co-3-mercaptopropionate).  

PubMed

A novel thermophilic bacterium, strain K14T, capable of degrading poly(3-hydroxybutyrate) as well as copolymers containing 3-hydroxybutyrate and 3-mercaptopropionate linked by thioester bonds, was isolated. 16S rDNA sequence analysis showed that strain DhA-71, a dehydroabietic acid-degrading bacterium, was the nearest phylogenetic neighbour and that both strains should be placed as members of a newly created genus, Schlegelella gen. nov., in the Rubrivivax subgroup of the beta-Proteobacteria. Strain K14T (= LMG 21644T = DSM 15344T) is proposed as the type strain of Schlegelella thermodepolymerans gen. nov., sp. nov. Its phylogenetic, morphological, biochemical and chemotaxonomic characteristics are described in detail. PMID:12892145

Elbanna, Khaled; Lütke-Eversloh, Tina; Van Trappen, Stefanie; Mergaert, Joris; Swings, Jean; Steinbüchel, Alexander

2003-07-01

198

Surface Map Traffic Intent Displays and Net-Centric Data-link Communications for NextGen  

NASA Technical Reports Server (NTRS)

By 2025, U.S. air traffic is predicted to increase three fold and may strain the current air traffic management system, which may not be able to accommodate this growth. In response to this challenge, a revolutionary new concept has been proposed for U.S. aviation operations, termed the Next Generation Air Transportation System or "NextGen". Many key capabilities are being identified to enable NextGen, including the use of data-link communications. Because NextGen represents a radically different approach to air traffic management and requires a dramatic shift in the tasks, roles, and responsibilities for the flight deck, there are numerous research issues and challenges that must be overcome to ensure a safe, sustainable air transportation system. Flight deck display and crew-vehicle interaction concepts are being developed that proactively investigate and overcome potential technology and safety barriers that might otherwise constrain the full realization of NextGen. The paper describes simulation research, conducted at National Aeronautics and Space Administration (NASA) Langley Research Center, examining data-link communications and traffic intent data during envisioned four-dimensional trajectory (4DT)-based and equivalent visual (EV) surface operations. Overall, the results suggest that controller pilot data-link communications (CPDLC) with the use of mandatory pilot read-back of all clearances significantly enhanced situation awareness for 4DT and EV surface operations. The depiction of graphical traffic state and intent information on the surface map display further enhanced off-nominal detection and pilot qualitative reports of safety and awareness.

Shelton, Kevin J.; Prinzel, Lawrence J., III; Jones, Denise R.; Allamandola, Angela S.; Arthur, Jarvis J., III; Bailey, Randall E.

2009-01-01

199

Telmaeshna paradoxica gen. et sp. nov., a new fossil dragonfly (Insecta: Odonata: Anisoptera) from the Yixian Formation, Liaoning, China  

Microsoft Academic Search

Telmaeshna paradoxica gen. et sp. nov., is described from the Upper Jurassic to Lower Cretaceous Yixian Formation, near Chaomidian Village, Beipiao City, Liaoning Province, China. It is included in the Anisoptera: Aeshnoptera: Aesh- nomorpha: Panaeshnida, on the basis of the following characters: strongly elongated pterostigma; well-defined anal loop and Rspl; undulated RP2, RP3\\/4 and MA; divided hypertriangle and discoidal triangle;

BINGLAN ZHANG; DONG REN; HONG PANG

2008-01-01

200

Mycosis of bandedwinged whitefly (Trialeurodes abutilonea) (Homoptera: aleyrodidae) caused by Orthomyces aleyrodis gen. & sp. nov. (Entomophthorales: Entomophthoraceae).  

PubMed

A new genus and species of fungus, Orthomyces aleyrodis Steinkraus, Humber & Oliver gen. & sp. nov. (Entomophthorales: Entomophthoraceae) is described. In 1994 and 1995, this fungus caused epizootics in high populations of bandedwinged whitefly (Trialeurodes abutilonea) on cotton and cocklebur in Alabama. In 1996, T. abutilonea populations were lower and no infected specimens were found. This is the first report of an entomophthoralean infecting an aleyrodid in the New World and the first report of entomophthoralean epizootics in whiteflies. PMID:9647695

Steinkraus, D C; Oliver, J B; Humber, R A; Gaylor, M J

1998-07-01

201

Experimental Investigations of the Ablation of Wire Arrays on the 250 kA GenASIS Machine  

Microsoft Academic Search

We present investigations of exploding wire experiments on a recently completed linear transformer driver (LTD) in the High Energy Density Physics laboratory at UCSD. The GenASIS machine delivers >250kA in 130ns to short circuit and >200kA to a wire array load, via a conical constant gap power feed. Measured load currents compare favorably to circuit modeling. This new generator facilitates

S. C. Bott; D. M. Haas; Y. Eshaq; U. Ueda; R. E. Madden; G. Collins; F. N. Beg

2008-01-01

202

New evidence of reproductive organs of Glossopteris based on permineralized fossils from Queensland, Australia. I. Ovulate organ Homevaleia gen. nov  

Microsoft Academic Search

This study describes Homevaleia gouldii H. Nishida, Pigg, Kudo et Rigby gen. et sp. nov., an ovule-bearing glossopterid organ, based on a combination of recently\\u000a collected permineralized specimens from the Late Permian Homevale Station locality in the Bowen Basin of Queensland, Australia,\\u000a and on previously studied material from the 1977 Gould and Delevoryas study. Homevaleia, which resembles the compression–impression genus

Harufumi Nishida; Kathleen B. Pigg; Kensuke Kudo; John F. Rigby

2007-01-01

203

A new fungicolous Scolecobasidium (hyphomycetes) and Caducirostrum gen. nov. (coelomycetes) from leaf litter in the UK and Italy  

Microsoft Academic Search

Summary  Two new microfungi, a fungicolous Scolecobasidium, S. rostricola sp. nov., colonising the ostiolar necks of a new coelomycete, Caducirostrum foliicola gen. & sp. nov., on leaf litter of Viburnum tinus, Arbutus unedo,\\u000a Prunus laurocerasus and P. lusitanica from the U.K. and Italy, are described, illustrated and compared with other relevant taxa. Rhabdostromina, with new combinations for Dendroseptoria arrhenatheri and D.

E. Punithalingam; Brian M. Spooner

204

Proposal of Yaniellaceae fam. nov., Yaniella gen. nov. and Sinobaca gen. nov. as replacements for the illegitimate prokaryotic names Yaniaceae Li et al. 2005, Yania Li et al. 2004, emend Li et al. 2005, and Sinococcus Li et al. 2006, respectively.  

PubMed

The prokaryotic generic names Yania Li et al. 2004 and Sinococcus Li et al. 2006 are illegitimate because they are later homonyms of the names Yania Roewer 1919 (Opiliones, Arachnida, Arthropoda, Animalia), Yania Huang 1997 (Lepidoptera: Hesperiidae) and Sinococcus Wu and Zheng 2000 (Homoptera: Coccomorpha) [Principle 2 of the Bacteriological Code (1990 Revision)]. Therefore, new generic names, Yaniella gen. nov. and Sinobaca gen. nov., are proposed for these taxa. In addition, a new family name, Yaniellaceae fam. nov., is proposed to accommodate Yaniella gen. nov. As a result, new combinations are required for the species to replace the illegitimate species names. PMID:18218962

Li, Wen-Jun; Zhi, Xiao-Yang; Euzéby, Jean P

2008-02-01

205

A rapid UPLC method for simultaneous determination of eleven components in ‘Ge-Gen-Qin-Lian’ decoction  

PubMed Central

Background: ‘Ge-Gen-Qin-Lian’ Decoction derived from ‘Shang-Han-Lun’ compiled by Zhang Zhongjing. It is widely used in the treatment of acute gastroenteritis, bacillary dysentery, virus diarrhea. This paper describes a sensitive and specific assay for the determination of the 11-marker compounds using ultra performance liquid chromatography (UPLC). Objective: To develop an UPLC method for simultaneous determination of 11 bioactive compounds in ‘Ge-Gen-Qin-Lian’ preparations. Materials and Methods: The chromatography analysis was performed on an Agilent Proshell 120 EC-C18 column (4.6 × 50 mm, 2.7 ?m) at 30°C with a gradient elution of methanol, 0.5% formic acid and 0.5% ammonium acetate at a flow rate 1.0 ml/min and UV detected at 270 nm. Results: All calibration curves showed good linear regression (r ? 0.9993) within tested ranges. Limits of detection (LOD) and limits of quantification (LOQ) fell in the range between 0.0691-1.04 ?g/ml and 0.23–3.43 ?g/ml, respectively. The mean recovery of each herbal medicine ranged from 96.60 to 102.11%. Conclusion: The method was validated for repeatability, precision, stability, accuracy, and selectivity. The validated method was successfully applied to simultaneous analysis of these active components in ‘Ge-Gen-Qin-Lian’ decoction.

An, Rui; You, Lisha; Zhang, Yizhu; Wang, Xinhong; Ma, Yuemin

2014-01-01

206

AtGEN1 and AtSEND1, Two Paralogs in Arabidopsis, Possess Holliday Junction Resolvase Activity.  

PubMed

Holliday junctions (HJs) are physical links between homologous DNA molecules that arise as central intermediary structures during homologous recombination and repair in meiotic and somatic cells. It is necessary for these structures to be resolved to ensure correct chromosome segregation and other functions. In eukaryotes, including plants, homologs of a gene called XPG-like endonuclease1 (GEN1) have been identified that process HJs in a manner analogous to the HJ resolvases of phages, archaea, and bacteria. Here, we report that Arabidopsis (Arabidopsis thaliana), a eukaryotic organism, has two functional GEN1 homologs instead of one. Like all known eukaryotic resolvases, AtGEN1 and Arabidopsis single-strand DNA endonuclease1 both belong to class IV of the Rad2/XPG family of nucleases. Their resolvase activity shares the characteristics of the Escherichia coli radiation and UV sensitive C paradigm for resolvases, which involves resolving HJs by symmetrically oriented incisions in two opposing strands. This leads to ligatable products without the need for further processing. The observation that the sequence context influences the cleavage by the enzymes can be interpreted as a hint for the existence of sequence specificity. The two Arabidopsis paralogs differ in their preferred sequences. The precise cleavage positions observed for the resolution of mobile nicked HJs suggest that these cleavage positions are determined by both the substrate structure and the sequence context at the junction point. PMID:25037209

Bauknecht, Markus; Kobbe, Daniela

2014-09-01

207

Meeting Air Transportation Demand in 2025 by Using Larger Aircraft and Alternative Routing to Complement NextGen Operational Improvements  

NASA Technical Reports Server (NTRS)

A study was performed that investigates the use of larger aircraft and alternative routing to complement the capacity benefits expected from the Next Generation Air Transportation System (NextGen) in 2025. National Airspace System (NAS) delays for the 2025 demand projected by the Transportation Systems Analysis Models (TSAM) were assessed using NASA s Airspace Concept Evaluation System (ACES). The shift in demand from commercial airline to automobile and from one airline route to another was investigated by adding the route delays determined from the ACES simulation to the travel times used in the TSAM and re-generating new flight scenarios. The ACES simulation results from this study determined that NextGen Operational Improvements alone do not provide sufficient airport capacity to meet the projected demand for passenger air travel in 2025 without significant system delays. Using larger aircraft with more seats on high-demand routes and introducing new direct routes, where demand warrants, significantly reduces delays, complementing NextGen improvements. Another significant finding of this study is that the adaptive behavior of passengers to avoid congested airline-routes is an important factor when projecting demand for transportation systems. Passengers will choose an alternative mode of transportation or alternative airline routes to avoid congested routes, thereby reducing delays to acceptable levels for the 2025 scenario; the penalty being that alternative routes and the option to drive increases overall trip time by 0.4% and may be less convenient than the first-choice route.

Smith, Jeremy C.; Guerreiro, Nelson M.; Viken, Jeffrey K.; Dollyhigh, Samuel M.; Fenbert, James W.

2010-01-01

208

Near-threshold photoionization of germanium clusters in the 248-144nm region: ionization potentials for Gen  

NASA Astrophysics Data System (ADS)

We examine the photoionization thresholds of Gen (n=2-34) with a wide photon energy (5.0-8.6 eV) using a laser photoionization time-of-flight mass spectrometry. A high-output vacuum ultraviolet light generated with stimulated Raman scattering is used as the ionization light source in the energy above 6.0 eV. A characteristic size dependence of ionization potential (IP) with a maximum at n=10 is found for clusters smaller than 22 atoms. The rather high IP of Ge10 in comparison with its neighbors is consistent with the results on the photodissociation study of Gen+. We also find that IPs decrease rapidly from n=16 to 22, and then decrease at a much slower rate for larger clusters. These features in IPs are similar to those of Sin reported in our previous paper, except for the smaller IP gap of Gen at n 20. We discuss these results on IPs in relation to their electronic structure and stability.

Fuke, K.; Yoshida, S.

209

Description of Tersicoccus phoenicis gen. nov., sp. nov. isolated from spacecraft assembly clean room environments.  

PubMed

Two strains of aerobic, non-motile, Gram-reaction-positive cocci were independently isolated from geographically distinct spacecraft assembly clean room facilities (Kennedy Space Center, Florida, USA and Centre Spatial Guyanais, Kourou, French Guiana). A polyphasic study was carried out to delineate the taxonomic identity of these two isolates (1P05MA(T) and KO_PS43). The 16S rRNA gene sequences exhibited a high similarity when compared to each other (100 %) and lower than 96.7 % relatedness with Arthrobacter crystallopoietes ATCC 15481(T), Arthrobacter luteolus ATCC BAA-272(T), Arthrobacter tumbae DSM 16406(T) and Arthrobacter subterraneus DSM 17585(T). In contrast with previously described Arthrobacter species, the novel isolates maintained their coccidal morphology throughout their growth and did not exhibit the rod-coccus life cycle typically observed in nearly all Arthrobacter species, except A. agilis. The distinct taxonomic identity of the novel isolates was confirmed based on their unique cell-wall peptidoglycan type (A.11.20; Lys-Ser-Ala2) and polar lipid profile (presence of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, an unknown phospholipid and two unknown glycolipids). The G+C content of the genomic DNA was 70.6 mol%. The novel strains revealed MK-9(H2) and MK-8(H2) as dominant menaquinones and exhibited fatty acid profiles consisting of major amounts of anteiso-C15 : 0 and anteiso-C17 : 0 and moderate amounts of iso-C15 : 0 discriminating them again from closely related Arthrobacter species. Based on these observations, the authors propose that strains 1P05MA(T) and KO_PS43 be assigned into a separate genus Tersicoccus gen. nov. For this new taxon, comprising strains 1P05MA(T) and KO_PS43, we propose the name Tersicoccus phoenicis gen. nov., sp. nov. (the type species of Tersicoccus), represented by the type strain Tersicoccus phoenicis 1P05MA(T) ( = NRRL B-59547(T) = DSM 30849(T)). PMID:23223813

Vaishampayan, Parag; Moissl-Eichinger, Christine; Pukall, Rüdiger; Schumann, Peter; Spröer, Cathrin; Augustus, Angela; Roberts, Anne Hayden; Namba, Greg; Cisneros, Jessica; Salmassi, Tina; Venkateswaran, Kasthuri

2013-07-01

210

GenSo-EWS: a novel neural-fuzzy based early warning system for predicting bank failures.  

PubMed

Bank failure prediction is an important issue for the regulators of the banking industries. The collapse and failure of a bank could trigger an adverse financial repercussion and generate negative impacts such as a massive bail out cost for the failing bank and loss of confidence from the investors and depositors. Very often, bank failures are due to financial distress. Hence, it is desirable to have an early warning system (EWS) that identifies potential bank failure or high-risk banks through the traits of financial distress. Various traditional statistical models have been employed to study bank failures [J Finance 1 (1975) 21; J Banking Finance 1 (1977) 249; J Banking Finance 10 (1986) 511; J Banking Finance 19 (1995) 1073]. However, these models do not have the capability to identify the characteristics of financial distress and thus function as black boxes. This paper proposes the use of a new neural fuzzy system [Foundations of neuro-fuzzy systems, 1997], namely the Generic Self-organising Fuzzy Neural Network (GenSoFNN) [IEEE Trans Neural Networks 13 (2002c) 1075] based on the compositional rule of inference (CRI) [Commun ACM 37 (1975) 77], as an alternative to predict banking failure. The CRI based GenSoFNN neural fuzzy network, henceforth denoted as GenSoFNN-CRI(S), functions as an EWS and is able to identify the inherent traits of financial distress based on financial covariates (features) derived from publicly available financial statements. The interaction between the selected features is captured in the form of highly intuitive IF-THEN fuzzy rules. Such easily comprehensible rules provide insights into the possible characteristics of financial distress and form the knowledge base for a highly desired EWS that aids bank regulation. The performance of the GenSoFNN-CRI(S) network is subsequently benchmarked against that of the Cox's proportional hazards model [J Banking Finance 10 (1986) 511; J Banking Finance 19 (1995) 1073], the multi-layered perceptron (MLP) and the modified cerebellar model articulation controller (MCMAC) [IEEE Trans Syst Man Cybern: Part B 30 (2000) 491] in predicting bank failures based on a population of 3635 US banks observed over a 21 years period. Three sets of experiments are performed-bank failure classification based on the last available financial record and prediction using financial records one and two years prior to the last available financial statements. The performance of the GenSoFNN-CRI(S) network as a bank failure classification and EWS is encouraging. PMID:15109685

Tung, W L; Quek, C; Cheng, P

2004-05-01

211

Functional Allocation for Ground-Based Automated Separation Assurance in NextGen  

NASA Technical Reports Server (NTRS)

As part of an ongoing research effort into functional allocation in a NextGen environment, a controller-in-the-loop study on ground-based automated separation assurance was conducted at NASA Ames' Airspace Operations Laboratory in February 2010. Participants included six FAA front line managers, who are currently certified professional controllers and four recently retired controllers. Traffic scenarios were 15 and 30 minutes long where controllers interacted with advanced technologies for ground-based separation assurance, weather avoidance, and arrival metering. The automation managed the separation by resolving conflicts automatically and involved controllers only by exception, e.g., when the automated resolution would have been outside preset limits. Results from data analyses show that workload was low despite high levels of traffic, Operational Errors did occur but were closely tied to local complexity, and safety acceptability ratings varied with traffic levels. Positive feedback was elicited for the overall concept with discussion on the proper allocation of functions and trust in automation.

Prevot, Thomas; Mercer, Joey; Martin, Lynne; Homola, Jeffrey; Cabrall, Christopher; Brasil, Connie

2010-01-01

212

Using Game Theoretic Models to Predict Pilot Behavior in NextGen Merging and Landing Scenario  

NASA Technical Reports Server (NTRS)

In this paper, we present an implementation of the Semi Network-Form Game framework to predict pilot behavior in a merging and landing scenario. In this scenario, two aircraft are approaching to a freeze horizon with approximately equal distance when they become aware of each other via an ADS-B communication link that will be available in NextGen airspace. Both pilots want to gain advantage over the other by entering the freeze horizon earlier and obtain the first place in landing. They re-adjust their speed accordingly. However, they cannot simply increase their speed to the maximum allowable values since they are concerned with safety, separation distance, effort, possibility of being vectored-off from landing and possibility of violating speed constraints. We present how to model these concerns and the rest of the system using semi network-from game framework. Using this framework, based on certain assumptions on pilot utility functions and on system configuration, we provide estimates of pilot behavior and overall system evolution in time. We also discuss the possible employment of this modeling tool for airspace design optimization. To support this discussion, we provide a case where we investigate the effect of increasing the merging point speed limit on the commanded speed distribution and on the percentage of vectored aircraft.

Yildiz, Yildiray; Lee, Ritchie; Brat, Guillaume

2012-01-01

213

Mobilitalea sibirica gen. nov., sp. nov., a halotolerant polysaccharide-degrading bacterium.  

PubMed

A novel strictly anaerobic, halotolerant, organotrophic bacterium, strain P3M-3(T), was isolated from a microbial mat formed under the flow of hot water emerging from a 2775 m-deep well in Tomsk region (western Siberia, Russia). Cells of strain P3M-3(T) were straight and curved rods, 0.2-0.4 µm in width and 1.5-20 µm in length. Strain P3M-3(T) grew optimally at 37 °C, pH 7.0-7.5 and in a NaCl concentration of 15 g l(-1). Under optimum growth conditions, the doubling time was 1 h. The isolate was able to ferment a variety of mono-, di- and polysaccharides, including microcrystalline cellulose. Acetate, ethanol, H2 and CO2 were the main products of glucose fermentation. The DNA G+C content was 33.4 mol%. 16S rRNA gene-based phylogenetic analysis showed that strain P3M-3(T) was a member of family Lachnospiraceae, whose representatives are also found in Clostridium cluster XIVa. 16S rRNA gene sequence similarity with Clostridium jejuense HY-35-12(T), the closest relative, was 93.9%. A novel genus and species, Mobilitalea sibirica gen. nov., sp. nov., are proposed based on phylogenetic analysis and physiological properties of the novel isolate. The type strain of the type species is P3M-3(T) (?=?DSM 26468(T)?=?VKM B-2804(T)). PMID:24827706

Podosokorskaya, O A; Bonch-Osmolovskaya, E A; Beskorovaynyy, A V; Toshchakov, S V; Kolganova, T V; Kublanov, I V

2014-08-01

214

Methods for Estimating Environmental Effects and Constraints on NexGen: High Density Case Study  

NASA Technical Reports Server (NTRS)

This document provides a summary of the current methods developed by Metron Aviation for the estimate of environmental effects and constraints on the Next Generation Air Transportation System (NextGen). This body of work incorporates many of the key elements necessary to achieve such an estimate. Each section contains the background and motivation for the technical elements of the work, a description of the methods used, and possible next steps. The current methods described in this document were selected in an attempt to provide a good balance between accuracy and fairly rapid turn around times to best advance Joint Planning and Development Office (JPDO) System Modeling and Analysis Division (SMAD) objectives while also supporting the needs of the JPDO Environmental Working Group (EWG). In particular this document describes methods applied to support the High Density (HD) Case Study performed during the spring of 2008. A reference day (in 2006) is modeled to describe current system capabilities while the future demand is applied to multiple alternatives to analyze system performance. The major variables in the alternatives are operational/procedural capabilities for airport, terminal, and en route airspace along with projected improvements to airframe, engine and navigational equipment.

Augustine, S.; Ermatinger, C.; Graham, M.; Thompson, T.

2010-01-01

215

Kretzoiarctos gen. nov., the Oldest Member of the Giant Panda Clade  

PubMed Central

The phylogenetic position of the giant panda, Ailuropoda melanoleuca (Carnivora: Ursidae: Ailuropodinae), has been one of the most hotly debated topics by mammalian biologists and paleontologists during the last century. Based on molecular data, it is currently recognized as a true ursid, sister-taxon of the remaining extant bears, from which it would have diverged by the Early Miocene. However, from a paleobiogeographic and chronological perspective, the origin of the giant panda lineage has remained elusive due to the scarcity of the available Miocene fossil record. Until recently, the genus Ailurarctos from the Late Miocene of China (ca. 8–7 mya) was recognized as the oldest undoubted member of the Ailuropodinae, suggesting that the panda lineage might have originated from an Ursavus ancestor. The role of the purported ailuropodine Agriarctos, from the Miocene of Europe, in the origins of this clade has been generally dismissed due to the paucity of the available material. Here, we describe a new ailuropodine genus, Kretzoiarctos gen. nov., based on remains from two Middle Miocene (ca. 12–11 Ma) Spanish localities. A cladistic analysis of fossil and extant members of the Ursoidea confirms the inclusion of the new genus into the Ailuropodinae. Moreover, Kretzoiarctos precedes in time the previously-known, Late Miocene members of the giant panda clade from Eurasia (Agriarctos and Ailurarctos). The former can be therefore considered the oldest recorded member of the giant panda lineage, which has significant implications for understanding the origins of this clade from a paleobiogeographic viewpoint. PMID:23155439

Abella, Juan; Alba, David M.; Robles, Josep M.; Valenciano, Alberto; Rotgers, Cheyenn; Carmona, Raul; Montoya, Plinio; Morales, Jorge

2012-01-01

216

Bandoniozyma gen. nov., a Genus of Fermentative and Non-Fermentative Tremellaceous Yeast Species  

PubMed Central

Background Independent surveys across the globe led to the proposal of a new basidiomycetous yeast genus within the Bulleromyces clade of the Tremellales, Bandoniozyma gen. nov., with seven new species. Methodology/Principal Findings The species were characterized by multiple methods, including the analysis of D1/D2 and ITS nucleotide sequences, and morphological and physiological/biochemical traits. Most species can ferment glucose, which is an unusual trait among basidiomycetous yeasts. Conclusions/Significance In this study we propose the new yeast genus Bandoniozyma, with seven species Bandoniozyma noutii sp. nov. (type species of genus; CBS 8364T ?=? DBVPG 4489T), Bandoniozyma aquatica sp. nov. (UFMG-DH4.20T ?=? CBS 12527T ?=? ATCC MYA-4876T), Bandoniozyma complexa sp. nov. (CBS 11570T ?=? ATCC MYA-4603T ?=? MA28aT), Bandoniozyma fermentans sp. nov. (CBS 12399T ?=? NU7M71T ?=? BCRC 23267T), Bandoniozyma glucofermentans sp. nov. (CBS 10381T ?=? NRRL Y-48076T ?=? ATCC MYA-4760T ?=? BG 02-7-15-015A-1-1T), Bandoniozyma tunnelae sp. nov. (CBS 8024T ?=? DBVPG 7000T), and Bandoniozyma visegradensis sp. nov. (CBS 12505T ?=? NRRL Y-48783T ?=? NCAIM Y.01952T). PMID:23056233

Landell, Melissa Fontes; Crestani, Juliana; Pagnocca, Fernando Carlos; Sette, Lara Duraes; Passarini, Michel Rodrigo Zambrano; Rosa, Carlos Augusto; Brandao, Luciana R.; Pimenta, Raphael S.; Ribeiro, Jose Roberto; Garcia, Karina Marques; Lee, Ching-Fu; Suh, Sung-Oui; Peter, Gabor; Dlauchy, Denes; Fell, Jack W.; Scorzetti, Gloria; Theelen, Bart; Vainstein, Marilene H.

2012-01-01

217

Zhihengliuella halotolerans gen. nov., sp. nov., a novel member of the family Micrococcaceae.  

PubMed

The actinobacterial strain YIM 70185(T) was isolated from a saline soil sample collected from Qinghai province, north-west China, and subjected to a taxonomic investigation. Phylogenetic analysis based on 16S rRNA gene sequences revealed 93.5-96.4 % similarity to members of related genera in the family Micrococcaceae. In the phylogenetic dendrogram based on 16S rRNA gene sequence analysis, strain YIM 70185(T) formed a separate clade next to the genera Micrococcus and Citricoccus within the family Micrococcaceae. The peptidoglycan type was A4alpha, l-lys-l-ala-l-Glu. Cell-wall sugars contained glucose and tyvelose. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, an unknown phospholipid and an unknown glycolipid. The menaquinones were MK-9, MK-10 and MK-8 (molar ratio 5 : 2 : 1). The major fatty acids were ai-C(15 : 0) and i-C(15 : 0) and the DNA G+C content was 66.5 mol%. These chemotaxonomic profiles supported the assignment of strain YIM 70185(T) to a novel genus within the family Micrococcaceae. The name Zhihengliuella halotolerans gen. nov., sp. nov. is proposed. The type strain of Zhihengliuella halotolerans is YIM 70185(T) (=DSM 17364(T)=KCTC 19085(T)). PMID:17473251

Zhang, Yu-Qin; Schumann, Peter; Yu, Li-Yan; Liu, Hong-Yu; Zhang, Yue-Qin; Xu, Li-Hua; Stackebrandt, Erko; Jiang, Cheng-Lin; Li, Wen-Jun

2007-05-01

218

Development of Complexity Science and Technology Tools for NextGen Airspace Research and Applications  

NASA Technical Reports Server (NTRS)

The objective of this research by NextGen AeroSciences, LLC is twofold: 1) to deliver an initial "toolbox" of algorithms, agent-based structures, and method descriptions for introducing trajectory agency as a methodology for simulating and analyzing airspace states, including bulk properties of large numbers of heterogeneous 4D aircraft trajectories in a test airspace -- while maintaining or increasing system safety; and 2) to use these tools in a test airspace to identify possible phase transition structure to predict when an airspace will approach the limits of its capacity. These 4D trajectories continuously replan their paths in the presence of noise and uncertainty while optimizing performance measures and performing conflict detection and resolution. In this approach, trajectories are represented as extended objects endowed with pseudopotential, maintaining time and fuel-efficient paths by bending just enough to accommodate separation while remaining inside of performance envelopes. This trajectory-centric approach differs from previous aircraft-centric distributed approaches to deconfliction. The results of this project are the following: 1) we delivered a toolbox of algorithms, agent-based structures and method descriptions as pseudocode; and 2) we corroborated the existence of phase transition structure in simulation with the addition of "early warning" detected prior to "full" airspace. This research suggests that airspace "fullness" can be anticipated and remedied before the airspace becomes unsafe.

Holmes, Bruce J.; Sawhill, Bruce K.; Herriot, James; Seehart, Ken; Zellweger, Dres; Shay, Rick

2012-01-01

219

Victivallis vadensis gen. nov., sp. nov., a sugar-fermenting anaerobe from human faeces.  

PubMed

A novel strictly anaerobic, cellobiose-degrading bacterium, strain CelloT, was isolated from a human faecal sample by combining enrichments in liquid and soft-agar basal media. A noteworthy characteristic was its inability to grow on normal agar plates and in roll tubes. The cells were coccus shaped and non-motile, with an extracellular slime layer. Growth of strain CelloT occurred between 20 and 40degrees C, with optimal growth at 37 degrees C. The pH range for growth was 5-7.5 with an optimum at 6.5. In pure culture, strain CelloT could only grow on a variety of sugars. Glucose was converted to acetate, ethanol and H2. The doubling time on glucose was 0.5 h. In a syntrophic co-culture with Methanospirillum hungatei strain JF-1T, strain CelloT converted glucose to acetate and H2. The G+C content was 59.2 mol%. 16S rDNA analysis revealed that the closest relatives of strain CelloT were two uncultured bacteria from anaerobic digesters, both with 94% 16S rDNA sequence similarity. The closest cultured representatives belong to genera of the bacterial division 'Verrucomicrobia'. The name Victivallis vadensis gen. nov., sp. nov. is proposed for strain CelloT (=DSM 14823T =ATCC BAA-548T). PMID:12656175

Zoetendal, Erwin G; Plugge, Caroline M; Akkermans, Antoon D L; de Vos, Willem M

2003-01-01

220

Future projections of extreme precipitation using Advanced Weather Generator (AWE-GEN) over Peninsular Malaysia  

NASA Astrophysics Data System (ADS)

A stochastic downscaling methodology known as the Advanced Weather Generator, AWE-GEN, has been tested at four stations in Peninsular Malaysia using observations available from 1975 to 2005. The methodology involves a stochastic downscaling procedure based on a Bayesian approach. Climate statistics from a multi-model ensemble of General Circulation Model (GCM) outputs were calculated and factors of change were derived to produce the probability distribution functions (PDF). New parameters were obtained to project future climate time series. A multi-model ensemble was used in this study. The projections of extreme precipitation were based on the RCP 6.0 scenario (2081-2100). The model was able to simulate both hourly and 24-h extreme precipitation, as well as wet spell durations quite well for almost all regions. However, the performance of GCM models varies significantly in all regions showing high variability of monthly precipitation for both observed and future periods. The extreme precipitation for both hourly and 24-h seems to increase in future, while extreme of wet spells remain unchanged, up to the return periods of 10-40 years.

Syafrina, A. H.; Zalina, M. D.; Juneng, L.

2014-09-01

221

Eoetvoesia caeni gen. nov., sp. nov., isolated from an activated sludge system treating coke plant effluent.  

PubMed

A novel bacterium, PB3-7B(T), was isolated on phenol-supplemented inorganic growth medium from a laboratory-scale wastewater purification system that treated coke plant effluent. 16S rRNA gene sequence analysis revealed that strain PB3-7B(T) belonged to the family Alcaligenaceae and showed the highest pairwise sequence similarity to Parapusillimonas granuli Ch07(T) (97.5%), Candidimonas bauzanensis BZ59(T) (97.3%) and Pusillimonas noertemannii BN9(T) (97.2%). Strain PB3-7B(T) was rod-shaped, motile and oxidase- and catalase-positive. The predominant fatty acids were C(16?:?0), C(17?:?0) cyclo, C(19?:?0) cyclo ?8c and C(14?:?0) 3-OH, and the major respiratory quinone was Q-8. The G+C content of the genomic DNA of strain PB3-7B(T) was 59.7 mol%. The novel bacterium can be distinguished from closely related type strains based on its urease activity and the capacity for assimilation of glycerol and amygdalin. On the basis of the phenotypic, chemotaxonomic and molecular data, strain PB3-7B(T) is considered to represent a new genus and species, for which the name Eoetvoesia caeni gen. nov., sp. nov. is proposed. The type strain of Eoetvoesia caeni is PB3-7B(T) (?=?DSM 25520(T)?=?NCAIM B 02512(T)). PMID:24585374

Felföldi, Tamás; Vengring, Anita; Kéki, Zsuzsa; Márialigeti, Károly; Schumann, Peter; Tóth, Erika M

2014-06-01

222

Ercella succinigenes gen. nov., sp. nov., an anaerobic succinate-producing bacterium.  

PubMed

A novel anaerobic succinate-producing bacterium, strain ZWB(T), was isolated from sludge collected from a biogas desulfurization bioreactor (Eerbeek, the Netherlands). Cells were non-spore-forming, motile, slightly curved rods (0.4-0.5 µm in diameter and 2-3 µm in length), and stained Gram-negative. The temperature range for growth was 25-40 °C, with an optimum at 37 °C. The pH range for growth was 7.0-9.0, with an optimum at pH 7.5. Strain ZWB(T) was able to ferment glycerol and several carbohydrates mainly to H2, succinate and acetate. Sulfur and fumarate could be used as electron acceptors by strain ZWB(T). The G+C content of the genomic DNA was 37.6 mol%. The most abundant fatty acids were iso-C14 : 0 and iso-C16?:?0 DMA. On the basis of 16S rRNA gene sequence similarity, strain ZWB(T) belongs to the family Ruminococcaceae and it is distantly related to Saccharofermentans acetigenes JCM 14006(T) (92.1%). Based on the physiological features and phylogenetic analysis, strain ZWB(T) represents a novel species of a new genus, for which the name Ercella succinigenes gen. nov., sp. nov. is proposed. The type strain of Ercella succinigenes is ZWB(T) (?= DSM 27333(T)?= JCM 19283(T)). PMID:24776531

van Gelder, Antonie H; Sousa, Diana Z; Rijpstra, W Irene C; Damsté, Jaap S Sinninghe; Stams, Alfons J M; Sánchez-Andrea, Irene

2014-07-01

223

Katatopygia gen. n., a monophyletic branch segregated from Boletina (Diptera, Mycetophilidae)  

PubMed Central

Abstract The genus Katatopygia gen. n. is proposed for the Boletina erythropyga/punctus-group that was first introduced by Garrett (1924, 1925) and currently comprises eight described species. Molecular studies have strongly indicated that this group forms a monophyletic sister-group to a clade consisting of all other Boletina, Coelosia and Gnoriste, and its monophyly is supported by morphological data as well. The new genus includes the following species: Katatopygia antoma (Garrett, 1924), comb. n., Katatopygia antica (Garrett, 1924), comb. n., Katatopygia erythropyga (Holmgren, 1883), comb. n.,Katatopygia hissarica (Zaitzev & Polevoi, 2002), comb. n., Katatopygia magna (Garrett, 1925), comb. n., Katatopygia laticauda (Saigusa, 1968), comb. n., Katatopygia neoerythropyga (Zaitzev & Polevoi, 2002), comb. n. andKatatopygia sahlbergi (Lundström, 1906), comb. n., all transferred from Boletina. Katatopygia sahlbergi is found to be a senior synonym of Boletina punctus Garrett, 1925, syn. n. A phylogeny based on morphological data and using parsimony analysis yielded four most parsimonious trees where the new genus is retrieved as monophyletic with high support. Katatopygia neoerythropyga is found to be the sister-taxon to all other species that form two clades, one with Katatopygia sahlbergi-like species and one with Katatopygia erythropyga-like species. A key to males of Katatopygia is provided. PMID:22451790

Martinsson, Svante; Kjaerandsen, Jostein

2012-01-01

224

Reclassification of Promicromonospora pachnodae Cazemier et al. 2004 as Xylanimicrobium pachnodae gen. nov., comb. nov.  

PubMed

The recently described facultatively anaerobic Promicromonospora pachnodae is phylogenetically only moderately related to authentic members of Promicromonospora. P. pachnodae is closely related to Xylanibacterium ulmi and slightly less closely related to Xylanimonas cellulosilytica and Isoptericola variabilis (basonym Cellulosimicrobium variabile). Members of the different genera of Promicromonosporaceae have similar chemotaxonomic properties; they share the same peptidoglycan type (A4alpha) and have similar profiles of polar lipids, menaquinones, fatty acids and whole cell sugars. However, they differ from each other in the detailed amino acid composition of peptidoglycan, a taxonomically significant character that has previously been used in the delineation of actinobacterial genera. Recognized Promicromonospora species and Xylanibacterium ulmi exhibit the L-Lys-L-Ala-D-Glu type, Xylanimonas cellulosilytica and I. variabilis show the L-Lys-D-Asp type, whereas P. pachnodae has the L-Lys-L-Ser-D-Glu type. This property, together with the distinct phylogenetic position of Promicromonospora pachnodae, suggests a novel genus for the xylanolytic organism Xylanimicrobium pachnodae (Cazemier et al. 2004) gen. nov., comb. nov. PMID:15280318

Stackebrandt, Erko; Schumann, Peter

2004-07-01

225

Xylanimonas cellulosilytica gen. nov., sp. nov., a xylanolytic bacterium isolated from a decayed tree (Ulmus nigra).  

PubMed

A bacterial strain, designated XIL07T, isolated from a decayed tree, Ulmus nigra, in Salamanca (Spain) produced abundant cellulases and xylanases. The micro-organism was Gram-positive, aerobic, coccoid and non-motile. Growth was observed on many carbohydrates, including cellulose and xylan as the sole carbon sources. No growth was observed with acetate, citrate, gluconate, inositol, malate or mannitol as carbon sources. The strain showed very weak catalase activity. HPLC analysis of menaquinones revealed two peaks: the main peak corresponded with MK-9(H4) and the smaller one with MK-8(H4). The major fatty acid found was anteiso-C15:0 (12-methyl tetradecanoic acid). Mycolic acids were absent. The polar lipids detected were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. Peptidoglycan type was A4alpha, L-Lys-D-Asp. The cell-wall sugars detected were galactose and rhamnose. The complete 16S rDNA sequence of strain XIL07T was obtained and phylogenetic analysis based on the neighbour-joining method indicated that this bacterium belongs to the high-G + C-content Gram-positive bacteria and that the closest related genera are Promicromonospora and Cellulosimicrobium. The DNA G + C content was 73 mol%. According to the data obtained in this work, this bacterium belongs to a new genus in the family Promicromonosporaceae and the name Xylanimonas cellulosilytica gen. nov., sp. nov. is proposed; the type strain is strain XIL07T (=LMG 20990T =CECT 5975T). PMID:12656159

Rivas, Raúl; Sánchez, Manuel; Trujillo, Martha E; Zurdo-Piñeiro, José Luis; Mateos, Pedro F; Martínez-Molina, Eustoquis; Velázquez, Encarna

2003-01-01

226

Investigating contact toxicity of Geranium and Artemisia essential oils on Bemisia tabaci Gen.  

PubMed Central

Objective: Sweet potato whitefly, Bemisia tabaci Gen. (B. tabaci), is one of the most important pests of various greenhouse crops in Iran. Nowadays, chemical insecticides are broadly used for control of the pests that causes risk to consumer's health. For the first time, contact toxicity of Pelargonium roseum Andrews and Artemisia sieberi Besser essential oils on B. tabaci and its possible application against the whitefly was evaluated in 2012. Materials and Methods: Essential oil with concentrations of 2500, 1250, 125, and 12 ppm were used. Infested leaves of greenhouse cucumber were treated by mentioned concentrations. After 24 hours, mortality of B. tabaci was recorded and compared after correcting by Abbot's formula. Results: Results showed that all concentrations of the essential oil could significantly reduce population of B. tabaci compared with the control treatment. Phytotoxicity of the treated leaves were recorded after 24, 48, and 72 hours and compared with the control. Concentrations of 2500, 1250, and 125 ppm caused severe phytotoxicity on greenhouse cucumber leaves and therefore are not suitable for greenhouse application. Phytotoxicity of 12 ppm was relatively low. Conclusions: This data implicated suitable protective effects of the essential oils to the pest infestation. Therefore, essential oils distillated from Geranium and Artemisia could be applied to control B. tabaci in greenhouse cucumber at V/V 12 ppm. PMID:25050264

Yarahmadi, Fatemeh; Rajabpour, Ali; Zandi Sohani, Nooshin; Ramezani, Leila

2013-01-01

227

Tepidicella xavieri gen. nov., sp. nov., a betaproteobacterium isolated from a hot spring runoff.  

PubMed

Strains TU-16T and TU-18, two non-pigmented bacterial isolates with an optimum growth temperature of about 45 degrees C and an optimum pH of about 8.5-9.0, were recovered from the Furnas geothermal area on the Island of São Miguel in the Azores. Phylogenetic analysis of the 16S rRNA gene sequence of these strains indicated that they represent a novel species in a new genus of the phylum Betaproteobacteria. The major fatty acids of strains TU-16T and TU-18 were 16 : 0 and 18 : 1omega7c. Ubiquinone 8 was the major respiratory quinone and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The novel isolates were aerobic; thiosulfate was oxidized to sulfate in the presence of a metabolizable carbon source. The organism assimilated organic acids and amino acids, but did not assimilate carbohydrates or polyols. Based on phylogenetic analyses and physiological and biochemical characteristics, it is proposed that strain TU-16T (=LMG 23030T = CIP 108724T) represents the type strain of a novel species in a new genus, Tepidicella xavieri gen. nov., sp. nov. PMID:16585714

França, Luis; Rainey, Fred A; Nobre, M Fernanda; da Costa, Milton S

2006-04-01

228

Reclassification of Cellulosimicrobium variabile Bakalidou et al. 2002 as Isoptericola variabilis gen. nov., comb. nov.  

PubMed

As already depicted in the original publication, the type strain of the species Cellulosimicrobium variabile Bakalidou et al. 2002, DSM 10177(T), does not cluster unambiguously with the type species, Cellulosimicrobium cellulans DSM 43879(T), in phylogenetic analysis. Strain DSM 10177(T) is moderately related to the recently described species Xylanimonas cellulosilytica, Promicromonospora pachnodae and Xylanibacterium ulmi, forming a lineage that branches between C. cellulans and members of the genus Promicromonospora in most dendrograms generated on the basis of different algorithms and reference strains. The type strains of the two Cellulosimicrobium species resemble each other in morphology, composition of fatty acids, DNA G+C content, phospholipids and the presence of lysine in position 3 of the peptide subunit of peptidoglycan. However, the two strains differ from each other in cell-wall sugars and in the amino acid composition of the A4alpha-type peptidoglycan, which contains serine and aspartic acid in C. cellulans, whereas only aspartic acid is present in the interpeptide bridge of C. variabile. This type is also present in Xylanimonas cellulosilytica XIL07(T), but not in the neighbouring species P. pachnodae DSM 12657(T), which exhibits the L-lys-L-ser-D-Glu type. On the basis of distinct phylogenetic position and the amino acid composition of peptidoglycan, a novel genus and combination for C. variabile, Isoptericola variabilis gen. nov., comb. nov., is proposed. PMID:15143008

Stackebrandt, Erko; Schumann, Peter; Cui, Xiao-Long

2004-05-01

229

Genetic and Adverse Health Outcome Associations with Treatment Resistant Hypertension in GenHAT  

PubMed Central

Treatment resistant hypertension (TRH) is defined as uncontrolled hypertension (HTN) despite the use of ?3 antihypertensive medication classes or controlled HTN while treated with ?4 antihypertensive medication classes. Risk factors for TRH include increasing age, diminished kidney function, higher body mass index, diabetes, and African American (AA) race. Importantly, previous studies suggest a genetic role in TRH, although the genetics of TRH are largely understudied. With 2203 treatment resistant cases and 2354 treatment responsive controls (36% AA) from the Genetics of Hypertension Associated Treatment Study (GenHAT), we assessed the association of 78 candidate gene polymorphisms with TRH status using logistic regression. After stratifying by race and adjusting for potential confounders, there were 2 genetic variants in the AGT gene (rs699, rs5051) statistically significantly associated with TRH among white participants. The Met allele of rs699 and the G allele of rs5051 were positively associated with TRH: OR = 1.27?(1.12–1.44), P = 0.0001, and OR = 1.36?(1.20–1.53), P < 0.0001, respectively. There was no similar association among AA participants (race interaction P = 0.0004 for rs699 and P = 0.0001 for rs5051). This research contributes to our understanding of the genetic basis of TRH, and further genetic studies of TRH may help reach the goal of better clinical outcomes for hypertensive patients. PMID:24288596

Lynch, Amy I.; Irvin, Marguerite R.; Davis, Barry R.; Ford, Charles E.; Eckfeldt, John H.; Arnett, Donna K.

2013-01-01

230

Kretzoiarctos gen. nov., the oldest member of the giant panda clade.  

PubMed

The phylogenetic position of the giant panda, Ailuropoda melanoleuca (Carnivora: Ursidae: Ailuropodinae), has been one of the most hotly debated topics by mammalian biologists and paleontologists during the last century. Based on molecular data, it is currently recognized as a true ursid, sister-taxon of the remaining extant bears, from which it would have diverged by the Early Miocene. However, from a paleobiogeographic and chronological perspective, the origin of the giant panda lineage has remained elusive due to the scarcity of the available Miocene fossil record. Until recently, the genus Ailurarctos from the Late Miocene of China (ca. 8-7 mya) was recognized as the oldest undoubted member of the Ailuropodinae, suggesting that the panda lineage might have originated from an Ursavus ancestor. The role of the purported ailuropodine Agriarctos, from the Miocene of Europe, in the origins of this clade has been generally dismissed due to the paucity of the available material. Here, we describe a new ailuropodine genus, Kretzoiarctos gen. nov., based on remains from two Middle Miocene (ca. 12-11 Ma) Spanish localities. A cladistic analysis of fossil and extant members of the Ursoidea confirms the inclusion of the new genus into the Ailuropodinae. Moreover, Kretzoiarctos precedes in time the previously-known, Late Miocene members of the giant panda clade from Eurasia (Agriarctos and Ailurarctos). The former can be therefore considered the oldest recorded member of the giant panda lineage, which has significant implications for understanding the origins of this clade from a paleobiogeographic viewpoint. PMID:23155439

Abella, Juan; Alba, David M; Robles, Josep M; Valenciano, Alberto; Rotgers, Cheyenn; Carmona, Raül; Montoya, Plinio; Morales, Jorge

2012-01-01

231

Leisingera methylohalidivorans gen. nov., sp. nov., a marine methylotroph that grows on methyl bromide  

USGS Publications Warehouse

A marine methylotroph, designated strain MB2T, was isolated for its ability to grow on methyl bromide as a sole carbon and energy source. Methyl chloride and methyl iodide also supported growth, as did methionine and glycine betaine. A limited amount of growth was observed with dimethyl sulfide. Growth was also noted with unidentified components of the complex media marine broth 2216, yeast extract and Casamino acids. No growth was observed on methylated amines, methanol, formate, acetate, glucose or a variety of other substrates. Growth on methyl bromide and methyl iodide resulted in their oxidation to CO2 with stoichiometric release of bromide and iodide, respectively. Strain MB2T exhibited growth optima at NaCl and Mg2+ concentrations similar to that of seawater. Phylogenetic analysis of the 16S rDNA sequence placed this strain in the ??-Proteobacteria in proximity to the genera Ruegeria and Roseobacter. It is proposed that strain MB2T (= ATCC BAA-92T = DSM 14336T) be designated Leisingera methylohalidivorans gen. nov., sp. nov.

Schaefer, J. K.; Goodwin, K. D.; McDonald, I. R.; Murrell, J. C.; Oremland, R. S.

2002-01-01

232

Calculation of astrophysical reaction rate of 82Ge(n,?)83Ge  

NASA Astrophysics Data System (ADS)

The neutron capture reaction on a neutron-rich near closed-shell nucleus 82Ge may play an important role in the r-process following the fallout from nuclear statistical equilibrium in core-collapse supernovae. By carrying out a DWBA analysis for the experimental angular distribution of 82Ge(d, p)83Ge reaction we obtain the single particle spectroscopic factors, S2,5/2 and S0,1/2 for the ground and first excited states of 83Ge = 82Geotimesn, respectively. And then these spectroscopic factors are used to calculate the direct capture cross sections for the 82Ge(n, ?)83Ge reaction at energies of astrophysical interest. The optical potential for neutron scattering on unstable nucleus 82Ge is not known experimentally. We employed a real folding potential which was calculated by using the proper 82Ge density distribution and an effective nucleon-nucleon force DDM3Y. The neutron capture reactions on neutron-rich closed-shell nuclei are expected to be dominated by the direct capture to bound states. We will show that the direct capture rates on these nuclei are sensitive to the structure of the low-lying states.

Wang, Mian; Chen, Yong-Shou; Li, Zhi-Hong; Liu, Wei-Ping; Shu, Neng-Chuan

2009-03-01

233

Aurapex penicillata gen. sp. nov. from native Miconia theaezans and Tibouchina spp. in Colombia.  

PubMed

Conidiomata of a fungus resembling Chrysoporthe cubensis, a serious canker pathogen of Eucalyptus spp. (Myrtaceae, Myrtales) in tropical and subtropical parts of the world, was found on Eucalyptus grandis in Colombia. Fruiting structures of the fungus could be distinguished from those of C. cubensis by their distinctly orange conidiomatal necks. This fungus also was found on several plant species native to Colombia including Tibouchina urvilleana, T. lepidota and Miconia theaezans (Melastomataceae, Myrtales). Morphological comparisons, as well as those based on sequences of the ITS1/ITS2 region of the ribosomal DNA repeat and the beta-tubulin gene, were used to characterize this fungus. Its pathogenicity was assessed on various plants from which it has been collected, either in field or greenhouse trials. Phylogenetic analyses showed that isolates reside in a clade distinct from the four clades accommodating Chrysoporthe, Cryphonectria, Endothia and Rostraureum. Members of this clade are distinguished by the presence of orange conidiomatal necks with black bases and a unique internal stromatal structure. No teleomorph has been found for this fungus, for which we have provided the name Aurapex penicillata gen. sp. nov. A. penicillata produced only small lesions after inoculation on young T. urvilleana, M. theaezans and E. grandis trees and appears not to be a serious pathogen. PMID:16800308

Gryzenhout, Marieka; Myburg, Henrietta; Rodas, Carlos A; Wingfield, Brenda D; Wingfield, Michael J

2006-01-01

234

Canibacter oris gen. nov., sp. nov., isolated from an infected human wound.  

PubMed

A facultatively anaerobic, Gram-reaction-positive, catalase- and oxidase-negative, rod-shaped bacterium isolated from an infected human wound caused by a dog bite was characterized by phenotypic and molecular genetic methods. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMMIB Q2029717T was a member of the order Micrococcales of the class Actinobacteria, displaying 91.6% to 96% sequence similarity with members of the family Microbacteriaceae. Phylogentic trees generated by different algorithms indicated that the strain forms an independent phylogenetic line of descent that consistently clustered proximal to the base of the genus Leucobacter. Chemical studies revealed the presence of a cell-wall murein based on L-lysine (type B1?), major menaquinone (MK-10) and a DNA G+C content of 56.9 mol%. The distinct phylogenetic position, ribotyping and matrix-assisted laser desorption/ionization time-of-flight MS profiles and the significant phenotypic differences clearly separate strain IMMIB Q2029717T from its nearest phylogenetic neighbour and support its classification as a representative of a novel genus and species, with the suggested name Canibacter oris gen. nov., sp. nov. The type strain is IMMIB Q2029717T (=DSM 27064T=CCUG 64069T). PMID:24510975

Aravena-Román, M; Inglis, T J J; Siering, C; Schumann, P; Yassin, A F

2014-05-01

235

Thiorhodococcus minus, gen. nov., sp. nov., A new purple sulfur bacterium isolated from coastal lagoon sediments.  

PubMed

A new marine phototrophic purple sulfur bacterium (strain CE2203) was isolated in pure culture from a man-made coastal lagoon located on the Atlantic coast (Arcachon Bay, France). Single cells were coccus-shaped, did not contain gas vesicles, and were highly motile. Intracellular photosynthetic membranes were of the vesicular type. Bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series were present as photosynthetic pigments. Hydrogen sulfide, thiosulfate, elemental sulfur, and molecular hydrogen were used as electron donors during photolithotrophic growth under anoxic conditions, while carbon dioxide was utilized as carbon source. Acetate, propionate, lactate, glycolate, pyruvate, fumarate, succinate, fructose, sucrose, ethanol, and propanol were photoassimilated in the presence of hydrogen sulfide. During growth on sulfide, elemental sulfur globules were stored inside the cells. Chemotrophic growth under microoxic conditions in the dark was possible. The DNA base composition was 66.9 mol% G+C. Comparative sequence analysis of the 16S rRNA gene confirmed the membership of strain CE2203 in the family Chromatiaceae. Morphological characteristics of strain CE2203 indicated a close affiliation to the genera Thiocystis and Thiocapsa. However, the phylogenetic treeing revealed no closer relationship to Thiocystis spp. than to Thiocapsa roseopersicina or other known members of the Chromatiaceae. Consequently, strain CE2203 is proposed as the type strain of a new genus and species, Thiorhodococcus minus gen. nov., sp. nov. PMID:9211709

Guyoneaud, R; Matheron, R; Liesack, W; Imhoff, J F; Caumette, P

1997-07-01

236

Croceibacter atlanticus gen. nov., sp. nov., a novel marine bacterium in the family Flavobacteriaceae.  

PubMed

A bright, saffron-colored marine bacterium HTCC2559T was isolated from the Bermuda Atlantic Time Series station in the western Sargasso Sea, Atlantic Ocean by high throughput culturing methods and characterized by polyphasic approaches. Phenotypic data and phylogenetic analyses showed that the strain is a member of the family Flavobacteriaceae. The strain was gram-negative, non-motile, chemoheterotrophic, strictly aerobic, NaCl-requiring, rod-shaped cells that contain carotenoid pigments but not flexirubin. Several kinds of macromolecules (gelatin, DNA, starch, casein, and elastin) were degraded and carbohydrates, sugar alcohols, organic acids, and amino acids were utilized as sole carbon sources. The dominant fatty acids were branched or hydroxy acids, and 3-OH i17:0, i15:0, i15:1, and i17:1 omega9c were abundant. The DNA G+C content of the strain is 34.8 mol%. Phylogenetic analyses using three treeing algorithms based on 16S rRNA gene sequences revealed that the strain formed a very distinct lineage that is allied closely with several seawater environmental clones in the family Flavobacteriaceae. Therefore, it is proposed from the polyphasic studies that strain HTCC2559T (=ATCC BAA-628T = KCTC 12090T) belongs to a new genus and species named Croceibacter atlanticus gen. nov., sp. nov. PMID:12747413

Cho, Jang-Cheon; Giovannoni, Stephen J

2003-03-01

237

Mitsuaria chitosanitabida gen. nov., sp. nov., an aerobic, chitosanase-producing member of the 'Betaproteobacteria'.  

PubMed

Four strains (3001(T), 2, 12 and 13), which were isolated as chitosanase-producing bacteria from soil from Matsue city (Japan), were studied phenotypically, genotypically and phylogenetically. Based on sequence analysis of 16S rRNA genes, DNA G+C content (67.4-69.2 mol%), quinone type (UQ-8), major fatty acid composition (3-OH 10:0, 3-OH 14:0) and other phylogenetic studies, strains 3001(T), 12 and 13 were found to occupy a separate position in the 'Betaproteobacteria'. Roseateles depolymerans, Rubrivivax gelatinosus and Ideonella dechloratans were their closest neighbours (93-95% 16S rRNA gene sequence similarity). The 16S rRNA gene sequence and other characteristics suggested that strain 2 belonged to the genus Flavobacterium. DNA-DNA hybridization experiments supported the conclusion that strains 3001(T), 12 and 13 were of the same species (72-78% DNA hybridization) and only distantly related to I. dechloratans and R. gelatinosus. It is proposed that strains 3001(T), 12 and 13 represent a novel genus and species for which the name Mitsuaria chitosanitabida gen. nov., sp. nov. is proposed. The type strain of Mitsuaria chitosanitabida is 3001(T) (=IAM 14711(T)=ATCC BAA-476(T)). PMID:16166689

Amakata, Daiki; Matsuo, Yasuhiro; Shimono, Kumiko; Park, Jae Kweon; Yun, Choong Soo; Matsuda, Hideyuki; Yokota, Akira; Kawamukai, Makoto

2005-09-01

238

Caldimonas manganoxidans gen. nov., sp. nov., a poly(3-hydroxybutyrate)-degrading, manganese-oxidizing thermophile.  

PubMed

A poly(3-hydroxybutyrate) (PHB)-degrading, gram-negative, aerobic bacterium, strain HS(T), was isolated from a hot spring and chemotaxonomically and phylogenetically characterized. The oxidase-positive, weakly catalase-positive, non-pigmented cells (0.6 x 2.6 microm) exhibited a single polar flagellum and accumulated PHB granules. Strain HS(T) was capable of manganese oxidation. Highest growth rate was attained at 50 degrees C. The optimum pH for growth was 7-8. The major respiratory quinone was ubiquinone-8 and major cellular fatty acids were C16:0, C16:1 and C18:1. The G+C content of the DNA was 66.2 mol%. Comparative 16S rDNA analysis indicated that strain HS(T) is related to the Rubrivivax subgroup and the family Comamonadaceae. The nearest phylogenetic relatives were Ideonella dechloratans (92.1% similarity), Leptothrix discophora (93.6%), Roseateles depolymerans (92.4%) and Rubrivivax gelatinosus (92.2%). On the basis of its phylogenetic and phenotypic properties, it is proposed that this isolate be designated Caldimonas manganoxidans gen. nov., sp. nov.; the type strain is HS(T) (= JCM 10698T = IFO 16448T = ATCC BAA-369T). PMID:12054255

Takeda, Minoru; Kamagata, Yoichi; Ghiorse, William C; Hanada, Satoshi; Koizumi, Jun-ichi

2002-05-01

239

Caenibacterium thermophilum gen. nov., sp. nov., isolated from a thermophilic aerobic digester of municipal sludge.  

PubMed

A bacterial strain, N2-680(T) (=DSM 15264(T)=LMG 21760(T)), isolated from a thermophilic aerobic digester of municipal sludge, was characterized with respect to its morphology, physiology and taxonomy. Phenotypically, the isolate was a Gram-negative rod with a polar flagellum, catalase- and oxidase-positive, containing cytoplasmic inclusions of poly-beta-hydroxybutyrate and had an optimal growth temperature of about 47 degrees C. Strain N2-680(T) was unable to reduce nitrate and could use organic acids, amino acids and carbohydrates as single carbon sources. Chemotaxonomic analysis revealed that ubiquinone 8 was the major respiratory quinone of this organism and that phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids. At 50 degrees C, the major components in fatty acid methyl ester analysis were C(16 : 0) and cyclo-C(17 : 0). The highest 16S rDNA sequence identity of isolate N2-680(T) was to Leptothrix mobilis and Ideonella dechloratans (95.7 %) and to Rubrivivax gelatinosus and Aquabacterium commune (95.6 %). 16S rDNA sequence similarities to species of two related thermophilic genera, Caldimonas manganoxidans and Tepidimonas ignava, were lower (93.6 and 94.7 %). On the basis of phylogenetic analyses and physiological and chemotaxonomic characteristics, it is proposed that isolate N2-680(T) represents a new genus and species, for which the name Caenibacterium thermophilum gen. nov., sp. nov. is proposed. PMID:13130021

Manaia, Célia M; Nunes, Olga C; Nogales, Balbina

2003-09-01

240

A new captorhinid reptile, Gansurhinus qingtoushanensis, gen. et sp. nov., from the Permian of China  

NASA Astrophysics Data System (ADS)

Captorhinids, a clade of Paleozoic reptiles, are represented by a rich fossil record that extends from the Late Carboniferous into the Late Permian. Representatives of this clade dispersed from the equatorial regions of Laurasia into the temperate regions of Pangea during the Middle and Late Permian. This rich fossil record shows that there was an evolutionary trend from faunivorous to omnivorous and herbivorous feeding habits within this clade. The discovery of well-preserved captorhinid materials in the Middle Permian of China allows us to determine that the new taxon, Gansurhinus qingtoushanensis, gen. et sp. nov, is a member of Moradisaurinae, a clade of captorhinids with multiple tooth rows arranged in parallel. The presence of this moradisaurine in the Middle Permian of south central Asia leads us to suggest that paleogeographic changes during the Permian, with part of what is today China becoming a large peninsula of Pangea, allowed these early reptiles as well as other terrestrial vertebrates to extend their geographic ranges to this region of the Late Paleozoic supercontinent.

Reisz, Robert R.; Liu, Jun; Li, Jin-Ling; Müller, Johannes

2011-05-01

241

Thalassospira lucentensis gen. nov., sp. nov., a new marine member of the alpha-Proteobacteria.  

PubMed

A novel bacterium from the Mediterranean Sea was isolated under oligotrophic conditions at in situ temperature after prolonged continuous culture. The isolates were initially characterized by partial 16S rRNA gene sequencing. Similarity searches of one of the isolates, QMT2T, indicated high sequence identity to the well-characterized Rhodospirillum rubrum, [Aquaspirillum] itersonii and [Oceanospirillum] pusillum micro-organisms, which are representatives of the alpha-subclass of the Proteobacteria. The highest level of similarity of the complete 165 rRNA gene with respect to these microorganisms was 89%. Features such as the low similarities of 165 rRNA of QMT2T with its phylogenetically close neighbours, the distinct G+C content, and the differences in phenotypic features, including pigmentation, fatty acid composition, salt tolerance, the lack of bacteriochlorophyll a, and the capacity to use carbohydrates as carbon sources, are indicative of the novel nature of the isolate QMT2T among the alpha-Proteobacteria. This report describes the classification of strain QMT2T (= DSM 14000T = CECT 5390T) as a new genus and species, Thalassospira lucentensis gen. nov, sp. nov., in the family Rhodospirillaceae. PMID:12148640

López-López, Arantxa; Pujalte, María J; Benlloch, Susana; Mata-Roig, Manuel; Rosselló-Mora, Ramón; Garay, Esperanza; Rodríguez-Valera, Francisco

2002-07-01

242

Synthetic and Enhanced Vision Systems for NextGen (SEVS) Simulation and Flight Test Performance Evaluation  

NASA Technical Reports Server (NTRS)

The Synthetic and Enhanced Vision Systems for NextGen (SEVS) simulation and flight tests are jointly sponsored by NASA's Aviation Safety Program, Vehicle Systems Safety Technology project and the Federal Aviation Administration (FAA). The flight tests were conducted by a team of Honeywell, Gulfstream Aerospace Corporation and NASA personnel with the goal of obtaining pilot-in-the-loop test data for flight validation, verification, and demonstration of selected SEVS operational and system-level performance capabilities. Nine test flights (38 flight hours) were conducted over the summer and fall of 2011. The evaluations were flown in Gulfstream.s G450 flight test aircraft outfitted with the SEVS technology under very low visibility instrument meteorological conditions. Evaluation pilots flew 108 approaches in low visibility weather conditions (600 ft to 2400 ft visibility) into various airports from Louisiana to Maine. In-situ flight performance and subjective workload and acceptability data were collected in collaboration with ground simulation studies at LaRC.s Research Flight Deck simulator.

Shelton, Kevin J.; Kramer, Lynda J.; Ellis,Kyle K.; Rehfeld, Sherri A.

2012-01-01

243

GenSAA: A tool for advancing satellite monitoring with graphical expert systems  

NASA Technical Reports Server (NTRS)

During numerous contacts with a satellite each day, spacecraft analysts must closely monitor real time data for combinations of telemetry parameter values, trends, and other indications that may signify a problem or failure. As satellites become more complex and the number of data items increases, this task is becoming increasingly difficult for humans to perform at acceptable performance levels. At the NASA Goddard Space Flight Center, fault-isolation expert systems have been developed to support data monitoring and fault detection tasks in satellite control centers. Based on the lessons learned during these initial efforts in expert system automation, a new domain-specific expert system development tool named the Generic Spacecraft Analyst Assistant (GenSAA) is being developed to facilitate the rapid development and reuse of real-time expert systems to serve as fault-isolation assistants for spacecraft analysts. Although initially domain-specific in nature, this powerful tool will support the development of highly graphical expert systems for data monitoring purposes throughout the space and commercial industry.

Hughes, Peter M.; Luczak, Edward C.

1993-01-01

244

Saccharophagus degradans gen. nov., sp. nov., a versatile marine degrader of complex polysaccharides.  

PubMed

Gammaproteobacteria belonging and related to the genus Microbulbifer are an emerging group of complex carbohydrate-degrading marine bacteria. Previously, all of the representatives were placed within Microbulbifer or were unclassified. Recently, a new genus, Teredinibacter, represented by a single species, Teredinibacter turnerae, was formed to include an endosymbiotic branch of these organisms. In this study, based on 16S rRNA gene sequence similarity and phenotypic analyses, a new genus, Saccharophagus, is proposed to accommodate the most versatile marine carbohydrate degrader yet identified, Saccharophagus degradans gen. nov., sp. nov. 2-40(T) (=ATCC 43961(T)=DSM 17024(T)). S. degradans strain 2-40(T) can degrade 10 tested complex polysaccharides: agar, alginate, chitin, cellulose, fucoidan, laminarin, pectin, pullulan, starch and xylan. S. degradans 2-40(T) shares 90.5% 16S rRNA gene sequence similarity with the type strain of the Microbulbifer type species, Microbulbifer hydrolyticus IRE-31(T), and 91.5% with T. turnerae T7902(T), and can be further distinguished from members of these two genera by 16S rRNA gene cluster analysis, the ability to utilize 10 different complex polysaccharides as sole carbon sources, a significantly lower G+C content and differences in fatty acid content. The three genera of complex polysaccharide-degrading, marine bacteria now encompass 20 strains from diverse marine niches. PMID:16014479

Ekborg, Nathan A; Gonzalez, Jose M; Howard, Michael B; Taylor, Larry E; Hutcheson, Steven W; Weiner, Ronald M

2005-07-01

245

Impact of Library Preparation on Downstream Analysis and Interpretation of RNA-Seq Data: Comparison between Illumina PolyA and NuGEN Ovation Protocol  

PubMed Central

Objectives The sequencing by the PolyA selection is the most common approach for library preparation. With limited amount or degraded RNA, alternative protocols such as the NuGEN have been developed. However, it is not yet clear how the different library preparations affect the downstream analyses of the broad applications of RNA sequencing. Methods and Materials Eight human mammary epithelial cell (HMEC) lines with high quality RNA were sequenced by Illumina’s mRNA-Seq PolyA selection and NuGEN ENCORE library preparation. The following analyses and comparisons were conducted: 1) the numbers of genes captured by each protocol; 2) the impact of protocols on differentially expressed gene detection between biological replicates; 3) expressed single nucleotide variant (SNV) detection; 4) non-coding RNAs, particularly lincRNA detection; and 5) intragenic gene expression. Results Sequences from the NuGEN protocol had lower (75%) alignment rate than the PolyA (over 90%). The NuGEN protocol detected fewer genes (12–20% less) with a significant portion of reads mapped to non-coding regions. A large number of genes were differentially detected between the two protocols. About 17–20% of the differentially expressed genes between biological replicates were commonly detected between the two protocols. Significantly higher numbers of SNVs (5–6 times) were detected in the NuGEN samples, which were largely from intragenic and intergenic regions. The NuGEN captured fewer exons (25% less) and had higher base level coverage variance. While 6.3% of reads were mapped to intragenic regions in the PolyA samples, the percentages were much higher (20–25%) for the NuGEN samples. The NuGEN protocol did not detect more known non-coding RNAs such as lincRNAs, but targeted small and “novel” lincRNAs. Conclusion Different library preparations can have significant impacts on downstream analysis and interpretation of RNA-seq data. The NuGEN provides an alternative for limited or degraded RNA but it has limitations for some RNA-seq applications. PMID:23977132

Sun, Zhifu; Asmann, Yan W.; Nair, Asha; Zhang, Yuji; Wang, Liguo; Kalari, Krishna R.; Bhagwate, Aditya V.; Baker, Tiffany R.; Carr, Jennifer M.; Kocher, Jean-Pierre A.; Perez, Edith A.; Thompson, E. Aubrey

2013-01-01

246

Surgical Treatment of Patients Enrolled in the National Registry of Genetically Triggered Thoracic Aortic Conditions (GenTAC)  

PubMed Central

Background Genetic disorders are an important cause of thoracic aortic aneurysms (TAAs) in young patients. Despite advances in the treatment of genetically triggered TAAs, the optimal syndrome-specific treatment approach remains undefined. We used data from the NIH-funded, multicenter National Registry of Genetically Triggered Thoracic Aortic Aneurysms and Cardiovascular Conditions (GenTAC) to characterize the contemporary surgical treatment of patients with genetically triggered TAAs. Methods GenTAC’s aim is to collect longitudinal clinical data and banked biospecimens from 2800 patients with genetically triggered TAAs. We analyzed data from all patients enrolled in GenTAC to date whose clinical data were available (n=606; mean age, 37.5 years). Results The patients’ primary diagnoses included Marfan syndrome (35.8%), bicuspid aortic valve with aneurysm (29.2%), and familial TAAs and dissections (10.7%). More than half of patients (56.4%) had undergone at least 1 operation; the most common indications were aneurysm (85.7%), valve dysfunction (65.8%), and dissection (25.4%). Surgical procedures included replacement of the aortic root (50.6%), ascending aorta (64.8%), aortic arch (27.9%), and descending or thoracoabdominal aorta (12.4%). Syndrome-specific differences in age, indications for surgery, and procedure type were identified. Conclusions Patients with genetically transmitted TAAs evaluated in tertiary care centers frequently undergo surgery. Aneurysm repairs most commonly involve the aortic root and ascending aorta; distal repairs are less common. Like TAAs themselves, complications of TAAs, including dissection and aortic valve dysfunction, are important indications for surgery. Future studies will focus on syndrome- and gene-specific phenotypes, biomarkers, treatments, and outcomes to improve the treatment of patients with TAAs. PMID:19699898

Song, Howard K.; Bavaria, Joseph E.; Kindem, Mark W.; Holmes, Kathryn W.; Milewicz, Dianna M.; Maslen, Cheryl L.; Pyeritz, Reed E.; Basson, Craig T.; Eagle, Kim; Tolunay, H. Eser; Kroner, Barbara L.; Dietz, Hal; Menashe, Victor; Devereux, Richard B.; Desvigne-Nickens, Patrice; Ravekes, William; Weinsaft, Jonathan W.; Brambilla, Donald; Stylianou, Mario P.; Hendershot, Tabitha; Mitchell, Megan S.; LeMaire, Scott A.

2011-01-01

247

Ciceribacter lividus gen. nov., sp. nov., isolated from rhizosphere soil of chick pea (Cicer arietinum L.).  

PubMed

The taxonomic position of strain MSSRFBL1(T), isolated from chickpea rhizosphere soil from Kannivadi, India, was determined. Strain MSSRFBL1(T) formed bluish black colonies, stained Gram-negative and was motile, aerobic, capable of fixing dinitrogen, oxidase-negative and catalase-positive. Q-10 was the major respiratory quinone. Major fatty acids of strain MSSRFBL1(T) were C18?:?1?7c and C19?:?0cyclo?8c. Minor amounts of C18?:?0, C12?:?0, C14?:?0 3-OH, C18?:?0 3-OH, C16?:?0, C16?:?1?6c/C16?:?1?7c, C17?:?0 3-OH and C20?:?1?7c were also present. Polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylcholine and two unidentified glycolipids. Bacteriohopane derivatives (BHD1 and 2), diplopterol, diploptene, bishomohopanediol, adenosylhopane and 2?-methyl bacteriohopanetetrol were the major hopanoids of strain MSSRFBL1(T). The genomic DNA G+C content was 71 mol%. EzTaxon-e-based blast analysis of the 16S rRNA gene indicated the highest similarity of strain MSSRFBL1(T) to Ensifer adhaerens LMG 20216(T) (97.3?%) and other members of the genus Ensifer (<96.9?%) in the family Rhizobiaceae of the class Alphaproteobacteria. However, phylogenetic analysis based on 16S rRNA, recA, thrC and dnaK gene sequences showed distinct out-grouping from the recognized genera of the family Rhizobiaceae. Based on phenotypic, genotypic and chemotaxonomic characters, strain MSSRFBL1(T) represents a novel species in a new genus in the family Rhizobiaceae for which the name Ciceribacter lividus gen. nov., sp. nov. is proposed. The type strain of Ciceribacter lividus is MSSRFBL1(T) (?=?DSM 25528(T)?=?KCTC 32403(T)). PMID:23907221

Kathiravan, R; Jegan, S; Ganga, V; Prabavathy, V R; Tushar, L; Sasikala, Ch; Ramana, Ch V

2013-12-01

248

Flaviflexus huanghaiensis gen. nov., sp. nov., an actinobacterium of the family Actinomycetaceae.  

PubMed

Strain H5(T) was isolated from a sediment sample collected from the coastal area of Qingdao, China. The cells were Gram-stain-positive, non-motile, straight or curved rods. The temperature range for growth was 20-37 °C and the pH for growth ranged from 6.5 to 9.0, with optimum growth occurring in the temperature range 28-30 °C and pH range 7.5-8.0. Growth occurred in the presence of 0-6% (w/v) NaCl (optimum, 0-2%). Strain H5(T) had MK-9, MK-9(H2) and MK-9(H4) as the major menaquinones and C18:1?9c, C16:0, C14:0, C18:0 and C16:1?9c as major fatty acids. The cell-wall peptidoglycan type was A5? l-Lys-l-Ala-l-Lys-d-Glu. The major polar lipids were phosphatidylglycerol (PG), an unknown phospholipid (PL1) and two unknown phosphoglycolipids (PGL1, PGL2). An unknown phospholipid (PL2) and two unknown glycolipids (GL1, GL2) were present in moderate to minor amounts in the polar lipid profile. The genomic DNA G+C content was 61.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain H5(T) represents a novel lineage in the family Actinomycetaceae. On the basis of phenotypic, physiological and molecular characteristics, it is proposed that the novel isolate should be classified as a novel species in a new genus: Flaviflexus huanghaiensis gen. nov., sp. nov., with strain H5(T) (?=?DSM 24315(T)?=CICC 10486(T)) as the type strain of the type species. PMID:23002046

Du, Zong-Jun; Miao, Ting-Ting; Lin, Xue-Zheng; Liu, Qian-Qian; Chen, Guan-Jun

2013-05-01

249

Visual Advantage of Enhanced Flight Vision System During NextGen Flight Test Evaluation  

NASA Technical Reports Server (NTRS)

Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment. Simulation and flight tests were jointly sponsored by NASA's Aviation Safety Program, Vehicle Systems Safety Technology project and the Federal Aviation Administration (FAA) to evaluate potential safety and operational benefits of SVS/EFVS technologies in low visibility Next Generation Air Transportation System (NextGen) operations. The flight tests were conducted by a team of Honeywell, Gulfstream Aerospace Corporation and NASA personnel with the goal of obtaining pilot-in-the-loop test data for flight validation, verification, and demonstration of selected SVS/EFVS operational and system-level performance capabilities. Nine test flights were flown in Gulfstream's G450 flight test aircraft outfitted with the SVS/EFVS technologies under low visibility instrument meteorological conditions. Evaluation pilots flew 108 approaches in low visibility weather conditions (600 feet to 3600 feet reported visibility) under different obscurants (mist, fog, drizzle fog, frozen fog) and sky cover (broken, overcast). Flight test videos were evaluated at three different altitudes (decision altitude, 100 feet radar altitude, and touchdown) to determine the visual advantage afforded to the pilot using the EFVS/Forward-Looking InfraRed (FLIR) imagery compared to natural vision. Results indicate the EFVS provided a visual advantage of two to three times over that of the out-the-window (OTW) view. The EFVS allowed pilots to view the runway environment, specifically runway lights, before they would be able to OTW with natural vision.

Kramer, Lynda J.; Harrison, Stephanie J.; Bailey, Randall E.; Shelton, Kevin J.; Ellis, Kyle K.

2014-01-01

250

Long-range correlation properties of coding and noncoding DNA sequences: GenBank analysis  

NASA Technical Reports Server (NTRS)

An open question in computational molecular biology is whether long-range correlations are present in both coding and noncoding DNA or only in the latter. To answer this question, we consider all 33301 coding and all 29453 noncoding eukaryotic sequences--each of length larger than 512 base pairs (bp)--in the present release of the GenBank to dtermine whether there is any statistically significant distinction in their long-range correlation properties. Standard fast Fourier transform (FFT) analysis indicates that coding sequences have practically no correlations in the range from 10 bp to 100 bp (spectral exponent beta=0.00 +/- 0.04, where the uncertainty is two standard deviations). In contrast, for noncoding sequences, the average value of the spectral exponent beta is positive (0.16 +/- 0.05) which unambiguously shows the presence of long-range correlations. We also separately analyze the 874 coding and the 1157 noncoding sequences that have more than 4096 bp and find a larger region of power-law behavior. We calculate the probability that these two data sets (coding and noncoding) were drawn from the same distribution and we find that it is less than 10(-10). We obtain independent confirmation of these findings using the method of detrended fluctuation analysis (DFA), which is designed to treat sequences with statistical heterogeneity, such as DNA's known mosaic structure ("patchiness") arising from the nonstationarity of nucleotide concentration. The near-perfect agreement between the two independent analysis methods, FFT and DFA, increases the confidence in the reliability of our conclusion.

Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Mantegna, R. N.; Matsa, M. E.; Peng, C. K.; Simons, M.; Stanley, H. E.

1995-01-01

251

Thermomonas haemolytica gen. nov., sp. nov., a gamma-proteobacterium from kaolin slurry.  

PubMed

Four aerobic, gram-negative bacterial strains isolated from kaolin slurry used in the production of paper were subjected to a polyphasic analysis and characterization to determine their taxonomic position. Analysis of the 16S rDNA sequences of the four strains revealed that they represent a new lineage within the gamma-Proteobacteria, related to the genera Xanthomonas, Pseudoxanthomonas, Stenotrophomonas, Luteimonas, Xylella and Rhodanobacter. Analysis of the quinone system, the polyamines, the fatty acids and the polar lipids revealed a combination of characteristics that is unique and not described for the phylogenetic relatives. The four strains contain a ubiquinone Q-8, spermidine as the major polyamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the predominant polar lipids, and a fatty acid profile with predominantly iso-branched fatty acids. The G+C content of the genomic DNA was determined to be within the narrow range 67.1-68.7 mol%. Determination of DNA relatedness, as well as riboprint band patterns and amplified fragment length polymorphism profiles, clearly demonstrated that the four strains are members of a single species. Antibiotic-susceptibility patterns were identical for the four strains. Although showing a high degree of similarites in physiological and biochemical patterns, each of the four strains could be distinguished from the others on the basis of a few biochemical characteristics. On the basis of the estimates of phylogenetic relationships derived from the 16S rDNA sequence analyses, the observed chemotaxonomic characteristics and other phenotypic traits, a new genus, Thermomonas gen. nov., and species, Thermomonas haemolytica sp. nov., are proposed for the strains A50-7-3T (= DSM 13605T = LMG 19653T), B 50-7-1 (= DSM 13598 = LMG 19655), D50-7-1 (= DSM 13610 = LMG 19656) and B50-8-1 (= DSM 13599 = LMG 19654), with strain A50-7-3T as the type strain. PMID:11931159

Busse, H J; Kämpfer, P; Moore, E R B; Nuutinen, J; Tsitko, I V; Denner, E B M; Vauterin, L; Valens, M; Rosselló-Mora, R; Salkinoja-Salonen, M S

2002-03-01

252

Stomatobaculum longum gen. nov., sp. nov., an obligately anaerobic bacterium from the human oral cavity  

PubMed Central

A strictly anaerobic Gram-stain-variable but positive by structure, non-spore-forming bacterium designated Lachnospiraceae bacterium ACC2 strain DSM 24645T was isolated from human subgingival dental plaque. Bacterial cells were 4–40 µm long non-motile rods, often swollen and forming curved filaments up to 200 µm. Cells contained intracellular, poorly crystalline, nanometre-sized iron- and sulfur-rich particles. The micro-organism was able to grow on yeast extract, trypticase peptone, milk, some sugars and organic acids. The major metabolic end-products of glucose fermentation were butyrate, lactate, isovalerate and acetate. The growth temperature and pH ranges were 30–42 °C and 4.9–7.5, respectively. Major fatty acids were C14?:?0, C14?:?0 DMA (dimethyl aldehyde), C16?:?0, C16?:?1?7c DMA. The whole-cell hydrolysate contained meso-diaminopimelic acid, indicating peptidoglycan type A1?. The DNA G+C content was calculated to be 55.05 mol% from the whole-genome sequence and 55.3 mol% as determined by HPLC. There were no predicted genes responsible for biosynthesis of respiratory lipoquinones, mycolic acids and lipopolysaccharides. Genes associated with synthesis of teichoic and lipoteichoic acids, diaminopimelic acid, polar lipids and polyamines were present. According to the 16S rRNA gene sequence phylogeny, strain DSM 24645T formed, together with several uncultured oral clones, a separate branch within the family Lachnospiraceae, with the highest sequence similarity to the type strain of Moryella indoligenes at 94.2?%. Based on distinct phenotypic and genotypic characteristics, we suggest that strain DSM 24645T represents a novel species in a new genus, for which the name Stomatobaculum longum gen. nov., sp. nov. is proposed. The type strain of Stomatobaculum longum is DSM 24645T (?=?HM-480T; deposited in BEI Resources, an NIH collection managed by the ATCC). PMID:22843721

Muller, Paul; Panikov, Nicolai; Mandalakis, Manolis; Hohmann, Tine; Hazen, Amanda; Fowle, William; Prozorov, Tanya; Bazylinski, Dennis A.

2013-01-01

253

Parapusillimonas granuli gen. nov., sp. nov., isolated from granules from a wastewater-treatment bioreactor.  

PubMed

A novel betaproteobacterium, designated strain Ch07(T), was isolated from granules from the wastewater-treatment bioreactor of an alcohol fermentation factory in South Korea. In order to determine its taxonomic position, the novel strain was characterized using a polyphasic approach. The new strain was Gram-negative, facultatively anaerobic, non-spore-forming, motile and short rod-shaped. 16S rRNA gene sequence analysis revealed that strain Ch07(T) belonged to the class Betaproteobacteria, being related to Pusillimonas noertemannii BN9(T) (gene sequence similarity 97.30 %), Achromobacter xylosoxidans subsp. xylosoxidans DSM 10346(T) (97.09 %), Bordetella pertussis DSM 5571(T) (97.01 %), Pigmentiphaga kullae DSM 13608(T) (96.68 %) and Castellaniella defragrans DSM 1214(T) (96.47 %). The results of DNA-DNA hybridization tests showed that reassociation values were less than 62 % with respect to these closely related type strains. Chemotaxonomic data showed that strain Ch07(T) possessed ubiquinone Q-8. The G+C content of the genomic DNA was 67.9+/-0.1 mol%. The major polyamine of strain Ch07(T) was putrescine. The major polar lipids of strain Ch07(T) were phosphatidylethanolamine, followed by diphosphatidylglycerol and phosphatidylglycerol. When strain Ch07(T) was incubated on tryptic soy agar, the major cellular fatty acids were C(16 : 0), C(17 : 0) cyclo, summed feature 3 (C(16 : 1)omega7c/iso C(15 : 0) 2-OH) and summed feature 5 (C(18 : 1)omega7c/omega9t/omega12t). The results of DNA-DNA hybridizations, in combination with the chemotaxonomic and physiological data, demonstrated that strain Ch07(T) represents a novel species of a new genus, for which the name Parapusillimonas granuli gen. nov., sp. nov. is proposed. The type strain of the type species is Ch07(T) (=KCTC 12668(T)=LMG 24012(T)). PMID:19671719

Kim, Yeon-Ju; Kim, Myung Kyum; Im, Wan-Taek; Srinivasan, Sathiyaraj; Yang, Deok-Chun

2010-06-01

254

Eiseniicola composti gen. nov., sp. nov., with antifungal activity against plant pathogenic fungi.  

PubMed

A Gram-negative, short rod-shaped bacterial strain, YC06271T, was isolated from the vermicompost (VC) collected at Masan, Korea and its taxonomic position was investigated by a polyphasic taxonomic approach. Strain YC06271T grew optimally at 28-30 degrees C and at pH 7.0-9.0. The 16S rRNA gene sequence of strain YC06271T was most closely related to members of the genera Bordetella (96.4-95.8 %), Achromobacter (96.0-95.7 %), Alcaligenes (96.0-94.2 %), Pusillimonas noertemannii (95.9 %), Pigmentiphaga (95.8-95.5 %) and less than 95.5 % similarity with the members of the other genera of the family Alcaligenaceae. Strain YC06271T contained ubiquinone-8 (Q-8) as the major respiratory quinone system and putrescine as the major polyamine. The major fatty acids of strain YC06271T were C16:1omega7c and/or C15:0 iso 2-OH and C16:0. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genomic DNA was 55.4 mol%. Phylogenetic analysis, biochemical, chemotaxonomic and phenotypic characteristics strongly supported the differentiation of strain YC06271T from the validly published genera of the family Alcaligenaceae. Therefore, it is proposed that strain YC06271T represents a novel species within a novel genus, with the name Eiseniicola composti gen. nov., sp. nov. The type strain is YC06271T (= KCTC 22250T = DSM 21045T). PMID:19734285

Yasir, Muhammad; Aslam, Zubair; Song, Geun Cheol; Jeon, Che Ok; Chung, Young Ryun

2010-01-01

255

Paralcaligenes ureilyticus gen. nov., sp. nov. isolated from soil of a Korean ginseng field.  

PubMed

A bacterial strain, designated GR24-5(T), was isolated from soil cultivated with Korean ginseng. Cells were Gram-negative, strictly aerobic, catalase- and oxidase-positive, non-spore-forming motile rods. Based on the 16S rRNA gene sequence, strain GR24-5(T) could be assigned to the family Alcaligenaceae. Strain GR24-5(T) showed the highest sequence similarities with Parapusillimonas granuli Ch07(T) (97.1%), Pusillimonas noertemannii BN9(T) (96.9%), Pigmentiphaga kullae DSM 13608(T) (96.5%), and Castellaniella defragrans 54Pin(T) (96.3%). Strain GR24-5(T) demonstrated a low DNA-DNA relatedness (23%) with P. granuli Ch07(T). The major respiratory quinone is ubiquinone 8 (Q-8) and the major fatty acids are C(16:0), C(17:0) cyclo, and summed feature 1 (C(14:0) 3-OH/iso-C(16:1) I/C(12:0) aide). Putrescine, spermidine, and 2-hydroxyputrescine are the major polyamines. The major polar lipids are phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, di-phosphatidylglycerol, and an unknown aminophospholipid. Polar lipid patterns of strain GR24-5(T) were unique in having a large amount of phosphatidylmethylethanolamine. Based on phylogenetic analysis and physiological and biochemical characteristics, strain GR245(T) represents a novel genus and species, for which the name Paralcaligenes ureilyticus gen. nov., sp. nov. is proposed. The type strain of P. aralcaligenes ureilyticus is GR24-5(T) (=KACC 13888 =DSM 24591(T)). PMID:21717340

Kim, Soo-Jin; Yoo, Seung-Hee; Weon, Hang-Yeon; Kim, Yi-Seul; Anandham, Rangasamy; Suh, Jang-Sun; Kwon, Soon-Wo

2011-06-01

256

Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome  

PubMed Central

A pure culture of an actinobacterium previously described as ‘Candidatus Rhodoluna lacicola’ strain MWH-Ta8 was established and deposited in two public culture collections. Strain MWH-Ta8T represents a free-living planktonic freshwater bacterium obtained from hypertrophic Meiliang Bay, Lake Taihu, PR China. The strain was characterized by phylogenetic and taxonomic investigations, as well as by determination of its complete genome sequence. Strain MWH-Ta8T is noticeable due to its unusually low values of cell size (0.05 µm3), genome size (1.43 Mbp), and DNA G+C content (51.5 mol%). Phylogenetic analyses based on 16S rRNA gene and RpoB sequences suggested that strain MWH-Ta8T is affiliated with the family Microbacteriaceae with Pontimonas salivibrio being its closest relative among the currently described species within this family. Strain MWH-Ta8T and the type strain of Pontimonas salivibrio shared a 16S rRNA gene sequence similarity of 94.3?%. The cell-wall peptidoglycan of strain MWH-Ta8T was of type B2? (B10), containing 2,4-diaminobutyric acid as the diamino acid. The predominant cellular fatty acids were anteiso-C15?:?0 (36.5?%), iso-C16?:?0 (16.5?%), iso-C15?:?0 (15.6?%) and iso-C14?:?0 (8.9?%), and the major (>10?%) menaquinones were MK-11 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The combined phylogenetic, phenotypic and chemotaxonomic data clearly suggest that strain MWH-Ta8T represents a novel species of a new genus in the family Microbacteriaceae, for which the name Rhodoluna lacicola gen. nov., sp. nov. is proposed. The type strain of the type species is MWH-Ta8T (?=?DSM 23834T?=?LMG 26932T). PMID:24984700

Schmidt, Johanna; Taipale, Sami J.; Doolittle, W. Ford; Koll, Ulrike

2014-01-01

257

Salinispirillum marinum gen. nov., sp. nov., a haloalkaliphilic bacterium in the family 'Saccharospirillaceae'.  

PubMed

A novel Gram-staining-negative, motile, non-pigmented, facultatively anaerobic, spirillum-shaped, halophilic and alkaliphilic bacterium, designated strain GCWy1(T), was isolated from water of the coastal-marine wetland Gomishan in Iran. The strain was able to grow at NaCl concentrations of 1-10?% (w/v) and optimal growth was achieved at 3?% (w/v). The optimum pH and temperature for growth were pH 8.5 and 30 °C, while the strain was able to grow at pH 7.5-10 and 4-40 °C. Phylogenetic analysis based on the comparison of the 16S rRNA gene sequence placed the isolate within the class Gammaproteobacteria as a separate deep branch, with 92.1?% or lower sequence similarity to representatives of the genera Saccharospirillum and Reinekea and less than 91.0?% sequence similarity with other remotely related genera. The major cellular fatty acids of the isolate were C18?:?1?7c, C16?:?0 and C17?:?0, and the major components of its polar lipid profile were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The cells of strain GCWy1(T) contained the isoprenoid quinones Q-9 and Q-8 (81?% and 2?%, respectively). The G+C content of the genomic DNA of this strain was 52.3 mol%. On the basis of 16S rRNA gene sequence analysis in combination with chemotaxonomic and phenotypic data, strain GCWy1(T) represents a novel species in a new genus in the family 'Saccharospirillaceae', order Oceanospirillales, for which the name Salinispirillum marinum gen. nov., sp. nov. is proposed. The type strain of the type species is GCWy1(T) (?=?IBRC-M 10765(T)?=?CECT 8342(T)). PMID:25062697

Shahinpei, Azadeh; Amoozegar, Mohammad Ali; Fazeli, Seyed Abolhassan Shahzadeh; Schumann, Peter; Ventosa, Antonio

2014-11-01

258

Metallibacterium scheffleri gen. nov., sp. nov., an alkalinizing gammaproteobacterium isolated from an acidic biofilm.  

PubMed

A Gram-stain-negative, non-motile, facultatively anaerobic, acid-tolerant rod, designated strain DKE6(T), was isolated from an acidic biofilm (pH 2.5) harvested in the pyrite mine Drei Kronen und Ehrt in Germany. The isolate grew optimally at pH 5.5, between 25 and 30 °C and only with casein as the carbon and energy source; although a variety of sugars were tested as growth substrates, none supported growth of the isolate. During casein consumption, strain DKE6(T) produced ammonium, which led to an alkalinization of the medium. This is a possible strategy to raise the pH in the direct vicinity of the cell and hence modulate the pH towards the growth optimum. The predominant fatty acids (>5?%) were iso-C11?:?0 3-OH, iso-C15?:?0, iso-C17?:?0 and iso-C17?:?1?9c. The DNA G+C content was 66.6?%. Strain DKE6(T) was not able to oxidize iron or thiosulfate. Iron reduction was detected. The isolate showed 93.3?% 16S rRNA gene sequence similarity to the most closely related cultivable strain, Dokdonella koreensis DS-123(T), but <93.2?% sequence similarity with other type strains of closely related type species of the Gammaproteobacteria. On the basis of physiological and biochemical data, the isolate is considered to represent a novel species of a new genus in the class Gammaproteobacteria, for which we propose the name Metallibacterium scheffleri gen. nov., sp. nov. The type strain of the type species is DKE6(T) (?=?DSM 24874(T)?=?JCM 17596(T)). PMID:22863988

Ziegler, Sibylle; Waidner, Barbara; Itoh, Takashi; Schumann, Peter; Spring, Stefan; Gescher, Johannes

2013-04-01

259

Povalibacter uvarum gen. nov., sp. nov., a polyvinyl-alcohol-degrading bacterium isolated from grapes.  

PubMed

Polyvinyl-alcohol-degrading bacteria were isolated from the fruit of a grape in Yokosuka, Japan. The isolated strain, Zumi 37(T), was a Gram-stain-negative, rod-shaped, motile, non-spore-forming and strictly aerobic chemo-organotroph, showing optimal growth at pH 7.5, 30 °C and 0.1% (w/v) NaCl. The major respiratory quinone was Q-8. The predominant fatty acids were iso-C(15?:?0), C(16?:?0) and C(16?:?1)?7c. The major polyamines were homospermidine and putrescine. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of the novel strain was 64.2 mol%. 16S rRNA gene sequence comparison revealed that strain Zumi 37(T) belongs to the family Sinobacteraceae within the class Gammaproteobacteria. Steroidobacter denitrificans DSM 18526(T) was the most closely related species with a validly published name, with 98.0% similarity based on 16S rRNA gene sequence comparison (and showed less than 87.5% sequence similarity to members of the genera Alkanibacter, Fontimonas, Hydrocarboniphaga, Nevskia and Solimonas with known 16S rRNA gene sequences). Phenotypes for growth under aerobic conditions and on complex media and major fatty acid composition, differed greatly from those of with comparatively high 16S rRNA gene sequence similarity. Based on phylogenetic, phenotypic and chemotaxonomic evidence, it is proposed that strain Zumi 37(T) represents a novel species in a new genus for which the name Povalibacter uvarum gen. nov., sp. nov. is proposed. The type strain of the type species is Zumi 37(T) (?=?JCM 18749(T)?=?DSM 26723(T)). PMID:24844263

Nogi, Yuichi; Yoshizumi, Masaki; Hamana, Koei; Miyazaki, Masayuki; Horikoshi, Koki

2014-08-01

260

Amphiplicatus metriothermophilus gen. nov., sp. nov., a thermotolerant alphaproteobacterium isolated from a hot spring.  

PubMed

A thermotolerant, Gram-strain-negative, non-spore-forming and strictly aerobic bacterium, designated GU51(T), was isolated from Guhai hot spring in Jimsar county, Xinjiang province, north-west China. Each cell of strain GU51(T) consisted of an oval body and two symmetrical long (3-6 µm) prosthecae. The strain moved by polar flagellum. Oxidase and catalase were produced. Strain GU51(T) grew within the ranges of 37-65 °C (optimum 48-50 °C), 0.5-7.5% (w/v) NaCl (optimum 2-3%) and pH 6.0-9.0 (optimum pH 7.5). The major respiratory quinone detected was ubiquinone 10 (U-10) and the genomic DNA G+C content was 66.7±0.4 mol%. Major fatty acids (>5%) were C(16?:?0), C(18?:?1)?7c and 11-methyl C(18?:?1)?7c. The polar lipids consisted of diphosphatidylglycerol, five glycolipids, phosphatidylglycerol and an unknown phospholipid. Phylogenetic analysis showed the closest relatives of strain GU51(T) were members of the genus Parvularcula with 92.3% 16S rRNA gene sequence similarity. On the basis of this polyphasic taxonomic characterization, it is suggested that strain GU51(T) represents a novel species of a new genus in the family 'Parvularculaceae', for which the name Amphiplicatus metriothermophilus gen. nov., sp. nov. is proposed. The type strain of the type species is GU51(T) (?=?CGMCC 1.12710(T)?=?JCM 19779(T)). PMID:24867176

Zhen-Li, Zhang; Xin-Qi, Zhang; Nan, Wu; Wen-Wu, Zhang; Xu-Fen, Zhu; Yi, Cao; Min, Wu

2014-08-01

261

Geothermomicrobium terrae gen. nov., sp. nov., a novel member of the family Thermoactinomycetaceae.  

PubMed

Strains YIM 77562(T) and YIM 77580, two novel Gram-staining-positive, filamentous bacterial isolates, were recovered from the Rehai geothermal field, Tengchong, Yunnan province, south-west China. Good growth was observed at 50-55 °C and pH 7.0. Aerial mycelium was absent on all media tested. Substrate mycelium was well-developed, long and moderately flexuous, and formed abundant, single, warty, ornamented endospores. Phylogenetic analysis of the 16S rRNA gene sequences of the two strains indicated that they belong to the family Thermoactinomycetaceae. Similarity levels between the 16S rRNA gene sequences of the two strains and those of type strains of members of the Thermoactinomycetaceae were 88.33-93.24?%; the highest sequence similarity was with Hazenella coriacea DSM 45707(T). In both strains, the predominant menaquinone was MK-7, the diagnostic diamino acid was meso-diaminopimelic acid and the major cellular fatty acids were iso-C14?:?0, iso-C15?:?0 and iso-C16?:?0. The major polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, unidentified polar lipids and unidentified phospholipids. The genomic DNA G+C contents of strains YIM 77562(T) and YIM 77580 were 45.5 and 44.2 mol%, respectively. DNA-DNA relatedness data suggest that the two isolates represent a single species. Based on phylogenetic analyses and physiological and biochemical characteristics, it is proposed that the two strains represent a single novel species in a new genus, Geothermomicrobium terrae gen. nov., sp. nov. The type strain of Geothermomicrobium terrae is YIM 77562(T) (?=?CCTCC AA 2011022(T)?=?JCM 18057(T)). PMID:24907264

Zhou, En-Min; Yu, Tian-Tian; Liu, Lan; Ming, Hong; Yin, Yi-Rui; Dong, Lei; Tseng, Min; Nie, Guo-Xing; Li, Wen-Jun

2014-09-01

262

Aquincola tertiaricarbonis gen. nov., sp. nov., a tertiary butyl moiety-degrading bacterium.  

PubMed

Strains L10(T), L108 and CIP I-2052 were originally obtained from methyl tert-butyl ether (MTBE)-contaminated groundwater and from a wastewater treatment plant, respectively. All share the ability to grow on tert-butanol, an intermediate of MTBE degradation. Cells are strictly aerobic, motile by a polar flagellum and exhibit strong pili formation. Poly beta-hydroxybutyrate (PHB) granules are formed. The DNA G+C content is 69-70.5 mol% and the main ubiquinone is Q-8. The major cellular fatty acids are 16 : 1 cis-9 and 16 : 0 and the only hydroxy fatty acid is 10 : 0 3-OH. The major phospholipids are phosphatidylethanolamine (PE) 16 : 1/16 : 1 and phosphatidylglycerol 16 : 0/16 : 1. A significant amount of PE 17 : 0/16 : 1 is present. The 16S rRNA gene sequences of these strains are almost identical and form a separate line of descent in the Rubrivivax-Roseateles-Leptothrix-Ideonella-Aquabacterium branch of the Betaproteobacteria with 97 % similarity to 16S rRNA genes of the type strains of Rubrivivax gelatinosus, Leptothrix mobilis and Ideonella dechloratans. However, physiological properties, DNA-DNA relatedness values and the phospholipid and cellular fatty acid profiles distinguish the novel isolates from the three closely related genera. Therefore, it is concluded that strains L10(T), L108 and CIP I-2052 represent a new genus and novel species for which the name Aquincola tertiaricarbonis gen. nov., sp. nov., is proposed. The type strain is strain L10(T) (=DSM 18512(T)=CIP 109243(T)). PMID:17551046

Lechner, Ute; Brodkorb, Danny; Geyer, Roland; Hause, Gerd; Härtig, Claus; Auling, Georg; Fayolle-Guichard, Françoise; Piveteau, Pascal; Müller, Roland H; Rohwerder, Thore

2007-06-01

263

Cascadiacarpa spinosa gen. et sp. nov. (Fagaceae): castaneoid fruits from the Eocene of Vancouver Island, Canada.  

PubMed

Documenting the paleodiversity of well-studied angiosperm families serves to broaden their circumscription while also providing a time-specific reference point to mark the first occurrence of characters and appearance of lineages. More than 80 anatomically preserved specimens of spiny, cupulate fruits in various developmental stages have been studied from the Eocene Appian Way locality of Vancouver Island, British Columbia, Canada. Details of internal anatomy and external morphology are known for the cupules, fruits, and pedicels. Cupule spines branch and are often borne in clusters. Cupules lack clear sutures and are adnate to a single nut that is enclosed entirely with the exception of the apical stylar protrusion of the pistil. A central hollow cylinder of vascular tissue can be seen extending up the peduncle to the base of the fruit and along the inner wall of the cupule. The fruit has a sclerotic outer pericarp that grades into a parenchymatous mesocarp and a sclerotic endocarp lining the locules. Early in development, the two locules are divided by a thin septum to which the ovules are attached. Only one seed develops to maturity as evidenced by an embryo occupying the locule alongside an abortive apical ovule. Three-dimensional reconstructions of these fruits have allowed for comparisons to both extinct and extant fagaceous taxa. The Appian Way fruits are most similar to extant Castanopsis species (Fagaceae) but differ in having only two locules. Cascadiacarpa spinosa gen. et sp. nov. Mindell, Stockey et Beard is the first occurence of a bipartite gynoecium and earliest known occurrence of hypogeous fruits in Fagaceae. The appearance of Casacadiacarpa in the Eocene of British Columbia supports a Paleogene radiation of the family. The numerous derived characters of these fruits show that evalvate, spiny, single-fruited cupules of Fagaceae were present in the Paleogene of North America. PMID:21636406

Mindell, Randal A; Stockey, Ruth A; Beard, Graham

2007-03-01

264

Evaluation of the Gen-Probe DNA probe for the detection of legionellae in culture  

SciTech Connect

A commercial DNA probe kit designed to detect rRNA from legionellae was evaluated for its ability to correctly discriminate between legionellae and non-legionellae taken from culture plates. The probe kit, made by the Gen-Probe Corp. (San Diego, Calif.), was radiolabeled with /sup 125/I, and probe bacterial RNA hybridization, detected in a simple one-tube system hybridization assay, was quantitated with a gamma counter. A total of 156 Legionella sp. strains were tested, of which 125 were Legionella pneumophila and the remainder were strains from 21 other Legionella spp. A total of 106 gram-negative non-legionellae, isolated from human respiratory tract (81%) and other body site (19%) specimens, were also tested; 14 genera and 28 species were represented. The probe easily distinguished all of the legionellae from the non-legionellae. The average legionellae/non-legionellae hybridization ratio was 42:1, and the lowest ratio was 2:1; a minor modification in the procedure increased the lowest ratio to 5:1. In addition to correctly identifying all Legionella species, the probe was able to separate some of the various species of Legionella. L. pneumophila strains hybridized more completely to the probe than did the other Legionella spp.; L. wadsworthii and L. oakridgensis hybridized only about 25% of the probe relative to L. pneumophila. Some strains of phenotypically identified L. pneumophila had much lower hybridization to the probe than other members of the species and may represent a new Legionella species. The simplicity of the technique and specificity of the probe make it a good candidate for confirming the identity of legionellae in culture.

Edelstein, P.H.

1986-03-01

265

Litoribrevibacter albus gen. nov. sp. nov., isolated from coastal seawater, Fujian province, China.  

PubMed

A Gram-stain negative, short rod-shaped aerobic bacterium with flagella, designated strain Y32(T), was isolated from coastal seawater in Xiamen, Fujian Province of China. 16S rRNA gene sequence comparisons showed that strain Y32(T) is a member of the family Oceanospirillaceae, forming a distinct lineage with species of the genus Litoribacillus. The 16S rRNA gene sequence similarities between strain Y32(T) and other strains were all less than 94.0 %. Strain Y32(T) was found to grow optimally at 28 °C, at pH 7.0-8.0 and in the presence of 4-5 % (w/v) NaCl. The major fatty acids were identified as Summed Feature 3 (comprising C16:1 ?7c and/or C16:1 ?6c, 49.4 %), C16:0 (17.7 %), C14:0 (6.9 %) and C18:1 ?9c (5.4 %). The major respiratory quinone was identified as ubiquinone-8 (Q-8). The major polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of strain Y32(T) was determined to be 55.6 mol%. According to its morphology, physiology, fatty acid composition, polar lipids composition and 16S rRNA gene sequence data, strain Y32(T) represents a novel species of a new genus in the family Oceanospirillaceae, for which the name Litoribrevibacter albus gen. nov. sp. nov. is proposed. The type strain of Litoribrevibacter albus is Y32(T) (=MCCC 1F01211(T)=NBRC 110071(T)). PMID:25193025

Li, Yi; Zhu, Hong; Lai, Qiliang; Lei, Xueqian; Zhang, Huajun; Chen, Zhangran; Zheng, Wei; Tian, Yun; Xu, Hong; Zheng, Tianling

2014-11-01

266

Hydrogenispora ethanolica gen. nov., sp. nov., an anaerobic carbohydrate-fermenting bacterium from anaerobic sludge.  

PubMed

An anaerobic, spore-forming, ethanol-hydrogen-coproducing bacterium, designated LX-BT, was isolated from an anaerobic sludge treating herbicide wastewater. Cells of strain LX-BT were non-motile rods (0.3-0.5×3.0-18.0 µm). Spores were terminal with a bulged sporangium. Growth occurred at 20-50 °C (optimum 37-45 °C), pH 5.0-8.0 (optimum pH 6.0-7.7) and 0-2.5% (w/v) NaCl. The strain could grow fermentatively on glucose, maltose, arabinose, fructose, xylose, ribose, galactose, mannose, raffinose, sucrose, pectin, starch, glycerol, fumarate, tryptone and yeast extract. The major end-products of glucose fermentation were acetate, ethanol and hydrogen. Yeast extract was not required but stimulated growth. Nitrate, sulfate, thiosulfate, elemental sulfur, sulfite, anthraquinone-2,6-disulfonate, fumarate and Fe (III) nitrilotriacetate were not used as terminal electron acceptors. The G+C content of the genomic DNA was 56.1 mol%. The major cellular fatty acids were anteiso-C15:0, iso-C14:0 and C16:0. The most abundant polar lipids of strain LX-BT were diphosphatidylglycerol and phosphatidylglycerol. 16S rRNA gene sequence analysis revealed that it belongs to an as-yet-unidentified taxon at the order- or class-level (OPB54) within the phylum Firmicutes, showing 86.5% sequence similarity to previously described species of the Desulfotomaculum cluster. The name Hydrogenispora ethanolica gen. nov., sp. nov. is proposed to accommodate strain LX-BT (=DSM 25471T=JCM 18117T=CGMCC 1.5175T) as the type strain. PMID:24554637

Liu, Yi; Qiao, Jiang-Tao; Yuan, Xian-Zheng; Guo, Rong-Bo; Qiu, Yan-Ling

2014-05-01

267

Fonticella tunisiensis gen. nov., sp. nov., isolated from a hot spring.  

PubMed

A strictly anaerobic, moderately thermophilic, halotolerant rod, designated BELH25(T), was isolated from a water sample of a Tunisian hot spring. Cells were non-motile, 2-6 µm long and 0.4-0.6 µm wide, appearing singly or in pairs. The isolate grew at 45-70 °C (optimum 55 °C), at pH 6.2-8.0 (optimum pH 7.0) and with 0-4% NaCl (optimum 0-2.0%). Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite were not used as terminal electron acceptors. Strain BELH25(T) used cellobiose, fructose, galactose, glucose, maltose, mannose, sucrose, starch and yeast extract as electron donors. The main fermentation products from glucose metabolism were formate, acetate, ethanol and CO2. The predominant cellular fatty acids were iso-C15:0, iso-C17:0 and anteiso-C15:0. The DNA G+C content was 37.2 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain BELH25(T) was most closely related to Caloramator viterbiensis JW/MS-VS5(T) and Fervidicella metallireducens AeB(T) (92.2 and 92.1% sequence similarity, respectively), and the isolate was positioned approximately equidistantly between these genera. Based on phenotypic, phylogenetic and chemotaxonomic characteristics, strain BELH25(T) is proposed to be a member of a novel species of a novel genus within the order Clostridiales, family Clostridiaceae, for which the name Fonticella tunisiensis gen. nov., sp. nov. is proposed. The type strain of the type species is BELH25(T) (=DSM 24455(T)=JCM 17559(T)). PMID:23024143

Fraj, Belkis; Ben Hania, Wajdi; Postec, Anne; Hamdi, Moktar; Ollivier, Bernard; Fardeau, Marie-Laure

2013-06-01

268

Pleomorphobacterium xiamenense gen. nov., sp. nov., a moderate thermophile isolated from a terrestrial hot spring.  

PubMed

An aerobic, motile, moderately thermophilic rod, designated strain CLW(T), was isolated from a terrestrial hot spring in an exposition garden in Xiamen City, Fujian Province, the People's Republic of China. Strain CLW(T) formed beige, dry colonies on solid 2216E medium and flocks in liquid medium. Cells were Gram-stain-negative, short rods (1.0-3.0 µm long and 0.4-0.6 µm wide) with six or more polar flagella. The temperature and pH for growth of strain CLW(T) were 28-65 °C (optimum, 50-58 °C) and pH 5.5-9.5 (optimum, pH 6.0-8.0). Growth occurred in the presence of 0.3-6.0?% NaCl (optimum 2.5-4.5?%). Phylogenetic analysis based on 16S rRNA gene sequences showed that the closest relative of the isolate was Amaricoccus kaplicensis Ben 101(T) (94.3?% sequence similarity). The DNA G+C content of strain CLW(T) was 72.2 mol%. The respiratory quinone was ubiquinone 10. The predominant polar lipids consisted of phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids (>10?%) were summed feature 8 (consisting of C18?:?1?7c and/or C18?:?1?6c), C18?:?1?7c 11-methyl and C18?:?0. Based on phylogenetic, physiological and biochemical data and DNA G+C content, strain CLW(T) is considered to represent a novel species of a new genus in the family Rhodobacteraceae, for which the name Pleomorphobacterium xiamenense gen. nov., sp. nov. is proposed. The type strain of the type species is CLW(T) (?=?LMG 26245(T)?=?CGMCC 1.10808(T)?=?MCCC 1A06272(T)). PMID:23041633

Yin, Decui; Chen, Liwei; Ao, Jingqun; Ai, Chunxiang; Chen, Xinhua

2013-05-01

269

Visual advantage of enhanced flight vision system during NextGen flight test evaluation  

NASA Astrophysics Data System (ADS)

Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment. Simulation and flight tests were jointly sponsored by NASA's Aviation Safety Program, Vehicle Systems Safety Technology project and the Federal Aviation Administration (FAA) to evaluate potential safety and operational benefits of SVS/EFVS technologies in low visibility Next Generation Air Transportation System (NextGen) operations. The flight tests were conducted by a team of Honeywell, Gulfstream Aerospace Corporation and NASA personnel with the goal of obtaining pilot-in-the-loop test data for flight validation, verification, and demonstration of selected SVS/EFVS operational and system-level performance capabilities. Nine test flights were flown in Gulfstream's G450 flight test aircraft outfitted with the SVS/EFVS technologies under low visibility instrument meteorological conditions. Evaluation pilots flew 108 approaches in low visibility weather conditions (600 feet to 3600 feet reported visibility) under different obscurants (mist, fog, drizzle fog, frozen fog) and sky cover (broken, overcast). Flight test videos were evaluated at three different altitudes (decision altitude, 100 feet radar altitude, and touchdown) to determine the visual advantage afforded to the pilot using the EFVS/Forward-Looking InfraRed (FLIR) imagery compared to natural vision. Results indicate the EFVS provided a visual advantage of two to three times over that of the out-the-window (OTW) view. The EFVS allowed pilots to view the runway environment, specifically runway lights, before they would be able to OTW with natural vision.

Kramer, Lynda J.; Harrison, Stephanie J.; Bailey, Randall E.; Shelton, Kevin J.; Ellis, Kyle K. E.

2014-06-01

270

Thermotunica guangxiensis gen. nov., sp. nov., isolated from mushroom residue compost.  

PubMed

A novel thermophilic actinomycete, designated AG2-7T, was isolated from mushroom residue compost in Guangxi University, Nanning, China. The strain grew optimally at 45-60 °C, at pH 7.0 and with 0-3.0% (w/v) NaCl. Vegetative mycelia were branched and whitish to pale yellow without fragmentation. Aerial mycelium was abundant, whitish and differentiated into long chains of spores, with a membranous structure or tunica partially covering the surface of aerial hyphae. The non-motile spores were oval in shape with a ridged surface. Strain AG-27T contained meso-diaminopimelic acid as the diagnostic diamino acid, and the whole-cell sugars were galactose and ribose. Major fatty acids were iso-C16:0 (27.51%), iso-C17:0 (10.47%) and anteiso-C17:0 (12.01%). MK-9(H4) was the predominant menaquinone. The polar phospholipids were diphosphatidylglycerol, ninhydrin-positive glycophospholipid, phosphatidylinositol, phosphatidylinositol mannoside, phosphatidylethanolamine, phosphatidylmethylethanolamine, an unknown phospholipid and unknown glucosamine-containing phospholipids. The G+C content of the genomic DNA was 63.6 mol%. 16S rRNA gene sequence analysis showed that the organism belonged to the family Pseudonocardiaceae, suborder Pseudonocardineae and showed more than 5% divergence from other members of the family. Based on the phenotypic and phylogenetic data, strain AG2-7T represents a novel species of a new genus in the family Pseudonocardiaceae, for which the name Thermotunica guangxiensis gen. nov., sp. nov. is proposed. The type strain of the type species is AG2-7T (=ATCC BAA-2499T=CGMCC 4.7099T). PMID:24488931

Wu, Hao; Lian, Yunpeng; Liu, Bin; Ren, Yanling; Qin, Peisheng; Huang, Fuchang

2014-05-01

271

Phylogenetic relationships among species of Williopsis and Saturnospora gen. nov. as determined from partial rRNA sequences.  

PubMed

Phylogenetic relationships among those yeast species that form saturn-shaped ascospores and which are assigned to the genera Williopsis and Pichia were estimated from their extent of nucleotide sequence divergence in three regions of ribosomal RNA. The Pichia species (P. dispora, P. saitoi, P. zaruensis and P. sp. nov.) are a closely clustered group only distantly related to Williopsis, and it is proposed that they be reassigned to Saturnospora gen. nov. The extent of divergence among Williopsis species (W. californica, W. mucosa, W. pratensis, W. saturnus and W. sp. nov.) is greater than that previously observed within other ascomycetous yeast genera. PMID:1796804

Liu, Z W; Kurtzman, C P

1991-07-01

272

Australasian sequestrate fungi 18: Solioccasus polychromus gen. & sp. nov., a richly colored, tropical to subtropical, hypogeous fungus.  

PubMed

Solioccasus polychromus gen. & sp. nov., the most brightly colored hypogeous fungus known, is described from Papua New Guinea and tropical northern Australia south into subtropical forests along the Queensland coast and coastal mountains to near Brisbane. Phylogenetic analysis of molecular data places it as a sister genus to Bothia in the Boletineae, a clade of predominantly ectomycorrhizal boletes. Ectomycorrhizal trees, such as members of the Myrtaceae (Eucalyptus, Corymbia, Lophostemon, Melaleuca spp.) and Allocasuarina littoralis, were present usually in mixture or in some cases dominant, so we infer some or all of them to be among the ectomycorrhizal hosts of S. polychromus. PMID:23709482

Trappe, James M; Castellano, Michael A; Halling, Roy E; Osmundson, Todd W; Binder, Manfred; Fechner, Nigel; Malajczuk, Nicholas

2013-01-01

273

Accuracy evaluation of ClimGen weather generator and daily to hourly disaggregation methods in tropical conditions  

NASA Astrophysics Data System (ADS)

Daily and sub-daily weather data are often required for hydrological and environmental modeling. Various weather generator programs have been used to generate synthetic climate data where observed climate data are limited. In this study, a weather data generator, ClimGen, was evaluated for generating information on daily precipitation, temperature, and wind speed at four tropical watersheds located in Hawai`i, USA. We also evaluated different daily to sub-daily weather data disaggregation methods for precipitation, air temperature, dew point temperature, and wind speed at M?kaha watershed. The hydrologic significance values of the different disaggregation methods were evaluated using Distributed Hydrology Soil Vegetation Model. MuDRain and diurnal method performed well over uniform distribution in disaggregating daily precipitation. However, the diurnal method is more consistent if accurate estimates of hourly precipitation intensities are desired. All of the air temperature disaggregation methods performed reasonably well, but goodness-of-fit statistics were slightly better for sine curve model with 2 h lag. Cosine model performed better than random model in disaggregating daily wind speed. The largest differences in annual water balance were related to wind speed followed by precipitation and dew point temperature. Simulated hourly streamflow, evapotranspiration, and groundwater recharge were less sensitive to the method of disaggregating daily air temperature. ClimGen performed well in generating the minimum and maximum temperature and wind speed. However, for precipitation, it clearly underestimated the number of extreme rainfall events with an intensity of >100 mm/day in all four locations. ClimGen was unable to replicate the distribution of observed precipitation at three locations (Honolulu, Kahului, and Hilo). ClimGen was able to reproduce the distributions of observed minimum temperature at Kahului and wind speed at Kahului and Hilo. Although the weather data generation and disaggregation methods were concentrated in a few Hawaiian watersheds, the results presented can be used to similar mountainous location settings, as well as any specific locations aimed at furthering the site-specific performance evaluation of these tested models.

Safeeq, Mohammad; Fares, Ali

2011-12-01

274

Notoatherix antiqua gen. et sp. nov., first fossil water snipe fly from the Late Jurassic of Australia (Diptera: Athericidae).  

PubMed

The first water snipe fly (Diptera: Tabanomorpha) fossil discovered in the Late Jurassic Talbragar Fish Bed in Australia is described and illustrated. Notoatherix antiqua gen. et sp. nov., described from a single wing specimen, is assigned to the family Athericidae based on the diagnostic feature of this family: the vein R2+3 ending very near to R1 (marginal cell closed). It is the first record of Athericidae from Australia and the oldest adult record of this family worldwide.  PMID:25283652

Oberprieler, Stefanie K; Yeates, David K

2014-01-01

275

A new genus and species of isanthid sea anemone (Cnidaria: Anthozoa: Actiniaria) from Chilean Patagonia, Anthoparactis fossii n. gen. et sp  

NASA Astrophysics Data System (ADS)

We describe a new genus and species of sea anemone from Chilean Patagonia. Anthoparactis fossii n. gen. et sp. adds another acontiate genus and species to the family Isanthidae Carlgren, 1938. Anthoparactis n. gen. differs from the other isanthid genera in having the same number of mesenteries distally and proximally, acontia with basitrichs only, and a column with verrucae distally. Anthoparactis fossii n. sp. differs from the most similar species, Isoparactis fionae Lauretta et al., 2013, in the number of cycles of mesenteries and tentacles, structures of the column, colour pattern of the oral disc, cnidae, and geographical distribution. Isanthidae now includes seven genera and 11 species.

Häussermann, Verena; Rodríguez, Estefanía

2014-09-01

276

Characterization of N2O-producing Xanthomonas-like isolates from biofilters as Stenotrophomonas nitritireducens sp. nov., Luteimonas mephitis gen. nov., sp. nov. and Pseudoxanthomonas broegbernensis gen. nov., sp. nov.  

PubMed

A group of yellow-pigmented isolates from ammonia-supplied biofilters showed an unusual denitrification reaction. All strains reduced nitrite but not nitrate without production of nitrogen (N2). The only product found was nitrous oxide (N2O). The strains were divided into two clusters and one separate strain by their fatty acid profiles, which were similar to the fatty acid profiles of the genera Xanthomonas and Stenotrophomonas. Analyses of the 165 rDNA sequences showed that these clusters and the separate strain form three independent lines within the Xanthomonas branch of the Proteobacteria. The evolutionary distances of the isolates to members of the related genera Xanthomonas, Stenotrophomonas and Xylella calculated by the 16S rDNA sequences led to the proposal of two new genera and three new species, Stenotrophomonas nitritireducens sp. nov., Luteimonas mephitis gen. nov., sp. nov. and Pseudoxanthomonas broegbernensis gen. nov., sp. nov. The type strains are Stenotrophomonas nitritireducens L2T (= DSM 12575T), Luteimonas mephitis B1953/27.1T (= DSM 12574T) and Pseudoxanthomonas broegbernensis B1616/1T (= DSM 12573T). PMID:10826814

Finkmann, W; Altendorf, K; Stackebrandt, E; Lipski, A

2000-01-01

277

Pyramidobacter piscolens gen. nov., sp. nov., a member of the phylum 'Synergistetes' isolated from the human oral cavity  

PubMed Central

Four strains of anaerobic, Gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group distinct from any species with validly published names. 16S rRNA and 23S rRNA gene sequence analyses and DNA–DNA reassociation data revealed that the strains constituted a novel group within the phylum ‘Synergistetes’ and were most closely related to Jonquetella anthropi. Two libraries of randomly cloned DNA were prepared from strain W5455T and were sequenced to provide a genome survey as a resource for metagenomic studies. A new genus and novel species, Pyramidobacter piscolens gen. nov., sp. nov., is proposed to accommodate these strains. The genus Pyramidobacter comprises strains that are anaerobic, non-motile, asaccharolytic bacilli that produce acetic and isovaleric acids and minor to trace amounts of propionic, isobutyric, succinic and phenylacetic acids as end products of metabolism. P. piscolens gen. nov., sp. nov. produced hydrogen sulphide but was otherwise largely biochemically unreactive. Growth was stimulated by the addition of glycine to broth media. The G+C content of the DNA of the type strain was 59?mol%. The type strain of Pyramidobacter piscolens sp. nov. is W5455T (=DSM 21147T=CCUG 55836T). PMID:19406777

Downes, Julia; Vartoukian, Sonia R.; Dewhirst, Floyd E.; Izard, Jacques; Chen, Tsute; Yu, Wen-Han; Sutcliffe, Iain C.; Wade, William G.

2009-01-01

278

Genome sequence and description of Timonella senegalensis gen. nov., sp. nov., a new member of the suborder Micrococcinae  

PubMed Central

Timonella senegalensis strain JC301T gen. nov., sp. nov. is the type strain of T. senegalensis gen. nov., sp. nov., a new species within the newly proposed genus Timonella. This bacterial strain was isolated from the fecal flora of a healthy Senegalese patient. In this report, we detail the features of this organism, together with the complete genome sequence and annotation. Timonella senegalensis strain JC301T exhibits the highest 16S rRNA similarity (95%) with Sanguibacter marinus, the closest validly published bacterial species. The genome of T. senegalensis strain JC301T is 3,010,102-bp long, with one chromosome and no plasmid. The genome contains 2,721 protein-coding genes and 72 RNA genes, including 5 rRNA genes. The genomic annotation revealed that T. senegalensis strain JC301T possesses the complete complement of enzymes necessary for the de novo biosynthesis of amino acids and vitamins (except for riboflavin and biotin), as well as the enzymes involved in the metabolism of various carbon sources, chaperone genes, and genes involved in the regulation of polyphosphate and glycogen levels. PMID:23991262

Mishra, Ajay Kumar; Lagier, Jean-Christophe; Robert, Catherine; Raoult, Didier; Fournier, Pierre-Edouard

2013-01-01

279

Chalicogloea cavernicola gen. nov., sp. nov. (Chroococcales, Cyanobacteria), from low-light aerophytic environments: combined molecular, phenotypic and ecological criteria.  

PubMed

This work characterizes a unicellular cyanobacterium with nearly spherical cells and thin-outlined sheaths that divide irregularly, forming small packets immersed in a diffluent mucilaginous layer. It was isolated growing on calcite speleothems and walls in a show cave in Collbató (Barcelona, Spain). Spectral confocal laser and transmission electron microscopy were used to describe the morphology, fine structure and thylakoid arrangement. The pigments identified were phycoerythrin, phycocyanin, allophycocyanin and chlorophyll a. Three-dimensional reconstructions, generated from natural fluorescence z-stacks, revealed a large surface area of nearly flat, arm-like thylakoidal membranes connected to each other and forming a unified structure in a way that, to our knowledge, has never been described before. Phylogenetic analyses using the 16S rRNA gene sequence showed 95% similarity to strain Chroococcus sp. JJCM (GenBank accession no. AM710384). The diacritical phenotypic features do not correspond to any species currently described, and the genetic traits support the strain being classified as the first member of an independent genus in the order Chroococcales and the family Chroococcaceae. Hence, we propose the name Chalicogloea cavernicola gen. nov., sp. nov. under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants. The type strain of Chalicogloea cavernicola is COLL 3(T) (=CCALA 975(T) =CCAP 1424/1(T)). PMID:23178723

Roldán, M; Ramírez, M; del Campo, J; Hernández-Mariné, M; Komárek, J

2013-06-01

280

New Australian stiletto flies: revision of Manestella Metz and description of Medomega gen. n. (Diptera, Therevidae, Agapophytinae)  

PubMed Central

Abstract The previously monotypic genus Manestella Metz, 2003 is revised with a single species, Manestella tristriata (Mann, 1933), redescribed and an additional 14 new species described: Manestella caesia sp. n., Manestella campestris sp. n., Manestella canities sp. n., Manestella cooloola sp. n., Manestella fumosa sp. n., Manestella incompleta sp. n., Manestella nubis sp. n., Manestella obscura sp. n., Manestella ocellaris sp. n., Manestella persona sp. n., Manestella poecilothorax sp. n., Manestella umbrapennis sp. n., Manestella vasta sp. n. and Manestella vespera sp. n. The putative sister genus to Manestella, Medomega gen. n., is described containing six new species: Medomega averyi sp. n., Medomega bailmeup sp. n., Medomega chlamydos sp. n., Medomega danielsi sp. n., Medomega gigasathe sp. n., and Medomega nebrias sp. n. Complete taxonomic descriptions were generated from a character matrix developed in Lucid Builder from which natural language descriptions (NLD) were parsed. Images of all species of Manestella and Medomega gen. n. are included, along with dichotomous keys to species. PMID:23226714

Winterton, Shaun L.; Lambkin, Christine L.

2012-01-01

281

Phylotranscriptomics: Saturated Third Codon Positions Radically Influence the Estimation of Trees Based on Next-Gen Data  

PubMed Central

Recent advancements in molecular sequencing techniques have led to a surge in the number of phylogenetic studies that incorporate large amounts of genetic data. We test the assumption that analyzing large number of genes will lead to improvements in tree resolution and branch support using moths in the superfamily Bombycoidea, a group with some interfamilial relationships that have been difficult to resolve. Specifically, we use a next-gen data set that included 19 taxa and 938 genes (?1.2M bp) to examine how codon position and saturation might influence resolution and node support among three key families. Maximum likelihood, parsimony, and species tree analysis using gene tree parsimony, on different nucleotide and amino acid data sets, resulted in largely congruent topologies with high bootstrap support compared with prior studies that included fewer loci. However, for a few shallow nodes, nucleotide and amino acid data provided high support for conflicting relationships. The third codon position was saturated and phylogenetic analysis of this position alone supported a completely different, potentially misleading sister group relationship. We used the program RADICAL to assess the number of genes needed to fix some of these difficult nodes. One such node originally needed a total of 850 genes but only required 250 when synonymous signal was removed. Our study shows that, in order to effectively use next-gen data to correctly resolve difficult phylogenetic relationships, it is necessary to assess the effects of synonymous substitutions and third codon positions. PMID:24148944

Breinholt, Jesse W.; Kawahara, Akito Y.

2013-01-01

282

Using the PhenoGen Website for “In Silico” Analysis of Morphine-Induced Analgesia: Identifying Candidate Genes  

PubMed Central

The identification of genes that contribute to polygenic (complex) behavioral phenotypes is a key goal of current genetic research. One approach to this goal is to combine gene expression information with genetic information, i.e., to map chromosomal regions that regulate gene expression levels. This approach has been termed “genetical genomics”, and, when used in conjunction with the identification of genomic regions (QTLs) that regulate the complex physiological trait under investigation, provides a strong basis for candidate gene discovery. In this paper, we describe the implementation of the genetical genomic/phenotypic approach to identify candidate genes for sensitivity to the analgesic effect of morphine in BXD recombinant inbred mice. Our analysis was performed “in silico”, using an online interactive resource called PhenoGen (http://phenogen.ucdenver.edu). We describe in detail the use of this resource, which identified a set of candidate genes, some of whose products regulate the cellular localization and activity of the mu opiate receptor. The results demonstrate how PhenoGen can be used to identify a novel set of genes that can be further investigated for their potential role in pain, morphine analgesia and/or morphine tolerance. PMID:21054686

Hoffman, Paula L.; Bennett, Beth; Saba, Laura M.; Bhave, Sanjiv V.; Carosone-Link, Phyllis J.; Hornbaker, Cheryl K.; Kechris, Katerina J.; Williams, Robert W.; Tabakoff, Boris

2010-01-01

283

A Controller-in-the Loop Simulation of Ground-Based Automated Separation Assurance in a NextGen Environment  

NASA Technical Reports Server (NTRS)

A controller-in-the-loop simulation was conducted in the Airspace Operations Laboratory (AOL) at the NASA Ames Research Center to investigate the functional allocation aspects associated with ground-based automated separation assurance in a far-term NextGen environment. In this concept, ground-based automation handled the detection and resolution of strategic and tactical conflicts and alerted the controller to deferred situations. The controller was responsible for monitoring the automation and managing situations by exception. This was done in conditions both with and without arrival time constraints across two levels of traffic density. Results showed that although workload increased with an increase in traffic density, it was still manageable in most situations. The number of conflicts increased similarly with a related increase in the issuance of resolution clearances. Although over 99% of conflicts were resolved, operational errors did occur but were tied to local sector complexities. Feedback from the participants revealed that they thought they maintained reasonable situation awareness in this environment, felt that operations were highly acceptable at the lower traffic density level but were less so as it increased, and felt overall that the concept as it was introduced here was a positive step forward to accommodating the more complex environment envisioned as part of NextGen.

Homola, J.; Prevot, Thomas; Mercer, Joey S.; Brasil, Connie L.; Martin, Lynne Hazel; Cabrall, C.

2010-01-01

284

Galaxitaenia toloi n. gen., n. sp. (Eucestoda: Pseudophyllidea) from Galaxias platei (Pisces: Osmeriformes, Galaxiidae), in the Patagonian region of Argentina.  

PubMed

Galaxitaenia n. gen. (Eucestoda: Pseudophyllidea) is proposed to accommodate Galaxitaenia toloi n. gen., n. sp. from Galaxias platei, a freshwater fish inhabiting Andean lakes in Argentine Patagonia. Galaxitaenia belongs to the Triaenophoridae because it possesses a marginal genital pore, a ventral uterine pore, and a follicular vitelline gland. The new genus can be distinguished from other triaenophorids by the following combination of characters: a scolex with a prominent rectangular apical disc without hooks, grooves, or indentations; neck present; segments wider than long to quadrangular; testes in 2 lateral fields, often connected anteriorly; cirrus unarmed; an ovary situated posteriorly; a vagina posterior to the cirrus sac; vitelline follicles medullary, in 2 ventral fields forming 2 wings interrupted medially; a uterus saccate to branched; and eggs without operculum. The types, distribution, and density of microtriches were analyzed on the surface of the tegument of scolex, neck, and immature segments. The presence of tumuli were observed on the apical disc of the scolex. Galaxitaenia toloi n. sp. is the first triaenophorid species recorded in a South American freshwater fish and the fourth helminth parasitizing the intestine of G. platei. PMID:17089762

Gil de Pertierra, Alicia A; Semenas, Liliana G

2005-08-01

285

Telmatocola sphagniphila gen. nov., sp. nov., a Novel Dendriform Planctomycete from Northern Wetlands  

PubMed Central

Members of the phylum Planctomycetes are common inhabitants of northern wetlands. We used barcoded pyrosequencing to survey bacterial diversity in an acidic (pH 4.0) Sphagnum peat sampled from the peat bog Obukhovskoye, European North Russia. A total of 21189 bacterial 16S rRNA gene sequences were obtained, of which 1081 reads (5.1%) belonged to the Planctomycetes. Two-thirds of these sequences affiliated with planctomycete groups for which characterized representatives have not yet been available. Here, we describe two organisms from one of these previously uncultivated planctomycete groups. One isolate, strain OB3, was obtained from the peat sample used in our molecular study, while another strain, SP2T (=DSM 23888T?=?VKM B-2710T), was isolated from the peat bog Staroselsky moss. Both isolates are represented by aerobic, budding, pink-pigmented, non-motile, spherical cells that are arranged in unusual, dendriform-like structures during growth on solid media. These bacteria are moderately acidophilic and mesophilic, capable of growth at pH 4.0–7.0 (optimum pH 5.0–5.5) and at 6–30°C (optimum 20–26°C). The preferred growth substrates are various heteropolysaccharides and sugars, the latter being utilized only if provided in low concentrations (?0.025%). In contrast to other described planctomycetes, strains SP2T and OB3 possess weak cellulolytic potential. The major fatty acids are C16:1?5c, C18:1?5c, C16:0, and C18:0. Characteristic lipids are the n-C31 polyunsaturated alkene (9–10 double bonds) and C30:1/C32:1 (?-1) hydroxy fatty acids. The G?+?C content of the DNA is 58.5–59.0?mol%. Strains SP2T and OB3 share identical 16S rRNA gene sequences, which exhibit only 86 and 87% similarity to those of Gemmata obscuriglobus and Zavarzinella formosa. Based on the characteristics reported here, we propose to classify these novel planctomycetes as representatives of a novel genus and species, Telmatocola sphagniphila gen. nov., sp. nov. PMID:22529844

Kulichevskaya, Irina S.; Serkebaeva, Yulia M.; Kim, Yongkyu; Rijpstra, W. Irene C.; Damste, Jaap S. Sinninghe; Liesack, Werner; Dedysh, Svetlana N.

2012-01-01

286

Fervidicella metallireducens gen. nov., sp. nov., a thermophilic, anaerobic bacterium from geothermal waters.  

PubMed

A strictly anaerobic, thermophilic bacterium, designated strain AeB(T), was isolated from microbial mats colonizing a run-off channel formed by free-flowing thermal water from a bore well (registered number 17263) of the Great Artesian Basin, Australia. Cells of strain AeB(T) were slightly curved rods (2.5-6.0x1.0 mum) that stained Gram-negative and formed spherical terminal to subterminal spores. The strain grew optimally in tryptone-yeast extract-Casamino acids medium at 50 degrees C (range 37-55 degrees C) and pH 7 (range pH 5-9). Strain AeB(T) grew poorly on yeast extract (0.2 %) and tryptone (0.2 %) as sole carbon sources, which were obligately required for growth on other energy sources. Growth of strain AeB(T) increased in the presence of various carbohydrates and amino acids, but not organic acids. End products detected from glucose fermentation were ethanol, acetate, CO2 and H2. In the presence of 0.2 % yeast extract, iron(III), manganese(IV), vanadium(V) and cobalt(III) were reduced, but not sulfate, thiosulfate, sulfite, elemental sulfur, nitrate or nitrite. Iron(III) was also reduced in the presence of tryptone, peptone, Casamino acids and amyl media (Research Achievement), but not starch, xylan, chitin, glycerol, ethanol, pyruvate, benzoate, lactate, acetate, propionate, succinate, glycine, serine, lysine, threonine, arginine, glutamate, valine, leucine, histidine, alanine, aspartate, isoleucine or methionine. Growth was inhibited by chloramphenicol, streptomycin, tetracycline, penicillin, ampicillin and NaCl concentrations >2 %. The DNA G+C content was 35.4+/-1 mol%, as determined by the thermal denaturation method. 16S rRNA gene sequence analysis indicated that strain AeB(T) is a member of the family Clostridiaceae, class Clostridia, phylum 'Firmicutes', and is positioned approximately equidistantly between the genera Sarcina, Anaerobacter, Caloramator and Clostridium (16S rRNA gene similarity values of 87.8-90.9 %). On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain AeB(T) is considered to represent a novel species in a new genus, for which the name Fervidicella metallireducens gen. nov., sp. nov. is proposed; the type strain is AeB(T) (=JCM 15555(T)=KCTC 5667(T)). PMID:19671710

Ogg, Christopher D; Patel, Bharat K C

2010-06-01

287

The Australian Monstrilloida (Crustacea: Copepoda) I. Monstrillopsis Sars, Maemonstrilla Grygier & Ohtsuka, and Australomonstrillopsis gen. nov.  

PubMed

Monstrilloid copepods were collected during zooplankton surveys in reef and coastal areas of Australia. Representatives of all four genera of the Monstrilloida (Monstrilla Dana, Monstrillopsis Sars, Cymbasoma Thompson, and Maemonstrilla Grygier & Ohtsuka) were recorded. In this contribution a taxonomic analysis of specimens belonging to the latter two genera is provided, and a new genus described. The genus Monstrillopsis was represented exclusively by male specimens, on the basis of which three new species are described: Mon. hastata sp. nov., Mon. boonwurrungorum sp. nov., and Mon. nanus sp. nov. These are distinguished from each other and previously described species of this genus by details of the genital complex (or genital apparatus), body size, ornamentation of the cephalic surface, number of caudal setae, and characteristic modifications of the fifth antennular segment. All have distinctive characters not associated with sexual modifications, which will ease the task of matching females collected in future studies. Australomonstrillopsis gen. nov. is proposed to accommodate a male specimen with a unique combination of characters including massively developed caudal rami, cephalic perioral protuberances, and absence of an inner seta on the first exopodal segment of legs 1-4, among other characters. The new genus is monotypic and contains A. crassicaudata sp. nov. Three of the four new species of Maemonstrilla (Mae. ohtsukai sp. nov., Mae. hoi sp. nov., and Mae. protuberans sp. nov.) belong to the Mae. hyottoko species group, and the remaining one, Mae. crenulata sp. nov., belongs to the Mae. turgida group. Each of the new species of Maemonstrilla from Australia can be distinguished from its known congeners by a unique combination of characters including the type of body reticulation, body size, antennule and body proportions, distinctive characters of the swimming legs, details of the antennular armature, and the presence/absence of a posteroventral process on the genital compound somite. With the addition of the four new species of Monstrillopsis and the four of Maemonstrilla described herein, the number of species in these genera has increased to 13 and 11 species, respectively. In no case did congeneric species co-occur, hinting that there may be a rich species diversity yet to be discovered within the Australian Monstrilloida. PMID:24871727

Suárez-Morales, Eduardo; Mckinnon, A David

2014-01-01

288

The Photosynthetic Apparatus and Its Regulation in the Aerobic Gammaproteobacterium Congregibacter litoralis gen. nov., sp. nov  

PubMed Central

Background There is accumulating evidence that in some marine environments aerobic bacteriochlorophyll a-producing bacteria represent a significant part of the microbial population. The interaction of photosynthesis and carbon metabolism in these interesting bacteria is still largely unknown and requires further investigation in order to estimate their contribution to the marine carbon cycle. Methodology/Principal Findings Here, we analyzed the structure, composition and regulation of the photosynthetic apparatus in the obligately aerobic marine gammaproteobacterium KT71T. Photoheterotrophically grown cells were characterized by a poorly developed lamellar intracytoplasmic membrane system, a type 1 light-harvesting antenna complex and a photosynthetic reaction center associated with a tetraheme cytochrome c. The only photosynthetic pigments produced were bacteriochlorophyll a and spirilloxanthin. Under semiaerobic conditions KT71T cells expressing a photosynthetic apparatus showed a light-dependent increase of growth yield in the range of 1.3–2.5 fold. The expression level of the photosynthetic apparatus depended largely on the utilized substrate, the intermediary carbon metabolism and oxygen tension. In addition, pigment synthesis was strongly influenced by light, with blue light exerting the most significant effect, implicating that proteins containing a BLUF domain may be involved in regulation of the photosynthetic apparatus. Several phenotypic traits in KT71T could be identified that correlated with the assumed redox state of growing cells and thus could be used to monitor the cellular redox state under various incubation conditions. Conclusions/Significance In a hypothetical model that explains the regulation of the photosynthetic apparatus in strain KT71T we propose that the expression of photosynthesis genes depends on the cellular redox state and is maximal under conditions that allow a balanced membrane redox state. So far, bacteria capable of an obligately aerobic, photosynthetic metabolism constitute a unique phenotype within the class Gammaproteobacteria, so that it is justified to propose a new genus and species, Congregibacter litoralis gen. nov, sp. nov., represented by the type strain KT71T (?=?DSM 17192T?=?NBRC 104960T). PMID:19287491

Spring, Stefan; Lunsdorf, Heinrich; Fuchs, Bernhard M.; Tindall, Brian J.

2009-01-01

289

Polycladomyces abyssicola gen. nov., sp. nov., a thermophilic filamentous bacterium isolated from hemipelagic sediment.  

PubMed

A novel filamentous bacterium, designated strain JIR-001(T), was isolated from hemipelagic sediment in deep seawater. This strain was non-motile, Gram-positive, aerobic, heterotrophic and thermophilic; colonies were of infinite form and ivory coloured with wrinkles between the centre and the edge of the colony on ISP2 medium. The isolate grew aerobically at 55-73 °C with the formation of aerial mycelia; spores were produced singly along the aerial mycelium. These morphological features show some similarities to those of the type strains of some species belonging to the family Thermoactinomycetaceae. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain JIR-001(T) belongs to the family Thermoactinomycetaceae within the class Bacilli. Similarity levels between the 16S rRNA gene sequence of strain JIR-001(T) and those of the type strains of Thermoactinomycetaceae species were 85.5-93.5%; highest sequence similarity was with Melghirimyces algeriensis NariEX(T). In the DNA-DNA hybridization assays between strain JIR-001(T) and its phylogenetic neighbours the mean hybridization levels with Melghirimyces algeriensis NariEX(T), Planifilum fimeticola H0165(T), Planifilum fulgidum 500275(T) and Planifilum yunnanense LA5(T) were 5.3-7.5, 2.3-4.7, 2.1-4.8 and 2.5-4.9%, respectively. The DNA G+C content of strain JIR-001(T) was 55.1 mol%. The major fatty acids were iso-C15:0, iso-C17:0, iso-C16:0 and C16:0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, glucolipid, phosphatidylserine, an amino-group containing phospholipid, an unknown phospholipid and two unknown lipids. The predominant menaquinone was MK-7 and the cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid and alanine. On the basis of phenotypic characteristics and 16S rRNA gene sequence comparisons, strain JIR-001(T) is considered to represent a novel species in a new genus of the family Thermoactinomycetaceae, for which the name Polycladomyces abyssicola gen. nov., sp. nov. is proposed. The type strain of Polycladomyces abyssicola is JIR-001(T) (=JCM 18147(T)=CECT 8074(T)). PMID:23024147

Tsubouchi, Taishi; Shimane, Yasuhiro; Mori, Kozue; Usui, Keiko; Hiraki, Toshiki; Tame, Akihiro; Uematsu, Katsuyuki; Maruyama, Tadashi; Hatada, Yuji

2013-06-01

290

History Sample 3 year curriculum in History for Bachelors/MD program 1Fall Gen Chem 1/Lab Bio Principles/L Calculus II Forum  

E-print Network

History Sample 3 year curriculum in History for Bachelors/MD program TOTAL CR 1Fall Gen Chem 1/Lab studies and lab cr 4 3 3 1 3 4 18 2Fall Organic Chem 1/L Genetics AMH 2020 US History from 1877 IDS 3932 19 2Spring Organic Chem 2/L HIS 3152 Historiography IDS 3932 Immigration (tt/Hist elective) IDS

Fernandez, Eduardo

291

USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 359 Fire as a Coarse Filter for Snags and Logs1  

E-print Network

unique coarse woody debris dynamics in low-, mixed-, and high-severity fire regimes. Moving towards moreUSDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 359 Fire as a Coarse Filter for Snags and Logs1 James K. Agee2 Abstract Fire played an important role in maintaining and creating conditions

Standiford, Richard B.

292

Rhombichthys intoccabilis, gen. et sp. nov. (Ellimmichthyiformes, Clupeomorpha, Teleostei), from the Cenomanian (Upper Cretaceous) of Ein Yabrud, Middle East: anatomical description and phylogenetic implications  

Microsoft Academic Search

A new double-armored member of the Ellimmichthyiformes (Clupeomorpha, Teleostei) is described from the Cenomanian (Upper Cretaceous) of Ein Yabrud, near Ramallah, Middle East. The anatomical description of Rhombichthys intoccabilis, gen. et sp. nov., is based on 13 subcomplete or incomplete acid-prepared specimens. This taxon shows several remarkable characters such as an important dorsoventral elongation of the lateral wings of the

Bouziane Khalloufi; René Zaragüeta-Bagils; Hervé Lelièvre

2010-01-01

293

Gen. Tech. Rep. PSW-58. Berkeley, CA: Pacific Southwest Forest and Range Experiment Station, Forest Service, U.S. Department of Agriculture; 1982. 123  

E-print Network

Gen. Tech. Rep. PSW-58. Berkeley, CA: Pacific Southwest Forest and Range Experiment Station, Forest of mortality and establishment. Through time, species populations are disappearing in some patches (disappearance from a patch) and which control local invasion (dispersal from outside the patch.) Extinction can

Standiford, Richard B.

294

281USDA Forest Service Gen.Tech.Rep. PSW-GTR-166. 1998. Systematic assessment and observation (survey, inventory) of forests in Latvia has been underway since the  

E-print Network

- toring Program in 1994. Assessments of forest ecosystems in Latvia show the alteration and disappearance281USDA Forest Service Gen.Tech.Rep. PSW-GTR-166. 1998. Abstract Systematic assessment and observation (survey, inventory) of forests in Latvia has been underway since the 1700's. Latvia's forests

Standiford, Richard B.

295

J. Phys. A: Math. Gen. 20 (1987) 1543-1555. Printed in the UK Hydrodynamic dispersion in a self-similar geometry  

E-print Network

J. Phys. A: Math. Gen. 20 (1987) 1543-1555. Printed in the UK Hydrodynamic dispersion in a self Hydrodynamic dispersion is a fundamental transport process in which a localised pulse of dynamically neutral reviews see, e.g., Bear 1971, Fried and Combamous 1971, Scheidegger 1974). The subtle interplay between

Redner, Sidney

296

and solvent in ion permeation. J. Gen. Physiol. (in the press). 16. Aqvist, J. & Luzhkov, V. Ion permeation mechanism of the potassium channel. Nature 404, 881884  

E-print Network

and solvent in ion permeation. J. Gen. Physiol. (in the press). 16. A°qvist, J. & Luzhkov, V. Ion permeation mechanism of the potassium channel. Nature 404, 881­884 (2000). 17. Luzhkov, V. B. & A° qvist, J). 30. Lu, T. et al. Probing ion permeation and gating in a Kþ channel with backbone mutations

Kah, Linda

297

Session D--Ecology of Fire on White Sands Missile Range--Boykin USDA Forest Service Gen. Tech. Rep. PSW-GTR-189 2008. 131  

E-print Network

Session D--Ecology of Fire on White Sands Missile Range--Boykin USDA Forest Service Gen. Tech. Rep. PSW-GTR-189 2008. 131 Response of Selected Plants to Fire on White Sands Missile Range, New Mexico1 related to many plants and communities within White Sands Missile Range. I began by identifying the known

Standiford, Richard B.

298

Wunderpus photogenicus n. gen. and sp., a new octopus from the shallow waters of the Indo-Malayan Archipelago (Cephalopoda: Octopodidae)  

Microsoft Academic Search

Wunderpus photogenicus n. gen. and n. sp. is a spectacular long-armed species that occurs on soft sediment habitats in shallow waters (typically less than 20 m deep) in Indo-Malayan waters. It is characterized by small eyes on elongate stalks, a long, conical papilla over each eye and a dramatic and fixed color pattern of white bars and spots over a

F. G. HOCHBERG; MARK D. NORMAN; JULIAN FINN

299

Poster Session--Stereo Photo Series for Quantifying Natural Fuels--Ottmar, Vihnanek, Wright USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 351  

E-print Network

central Alaska to central Brazil. Fire managers are the primary target audience of the natural fuels photo Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 351 Stereo Photo Series for Quantifying Natural Fuels series, although the data presented will also prove useful for scientists and managers in other natural

Standiford, Richard B.

300

Session H--NEPA Disclosure of Air Quality Impacts--Ahuja, Perrot USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008.  

E-print Network

Session H--NEPA Disclosure of Air Quality Impacts--Ahuja, Perrot USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. . 193 National Environmental Policy Act Disclosure of Air Quality Impacts air quality and has the potential to impact human health and quality of life. Public concern about

Standiford, Richard B.

301

Thomas, Robert B. 1989. Piecewise SALT sampling for estimating suspended sediment yields. Gen. Tech. Rep. PSW-114. Berkeley, CA: Pacific Southwest Forest and Range  

E-print Network

, probability sampling, measurement, SALT sampling Forest activities such as logging, road building, and mining#12;Thomas, Robert B. 1989. Piecewise SALT sampling for estimating suspended sediment yields. Gen, U.S. Department of Agriculture; 11 p. A probability sampling method called SALT (Selection At List

Standiford, Richard B.

302

A new porolepiform-like fish, Psarolepis romeri, gen. et sp. nov. (Sarcopterygii, Osteichthyes) from the Lower Devonian of Yunnan, China  

Microsoft Academic Search

A new sarcopterygian fish, Psarolepis, gen. nov. (Sarcopterygii, Osteichthyes) is described from the Lower Devonian of Eastern Yunnan, China. The new genus manifests many porolepiform-like features that are commonly used to distinguish porolepiforms from osteolepiforms, such as internasal cavity well developed, parasphenoid not protruding forward to ethmoidal region, vomeral area rectangular in shape and not meeting at median line, dorsal

Xiaobo Yu

1998-01-01

303

tEknolo Giavd ElinGEn FRost i JoRd 2007 1 Remote sensing of permafrost hazards in mountains  

E-print Network

tEknolo Giavd ElinGEn FRost i JoRd 2007 1 Remote sensing of permafrost hazards in mountains Fjernmåling av faremomenter ved permafrost i høyfjellsområder Andreas Kääb, Universitetet i Oslo (UiO) (kaeaeb ice involved. Norway with its significant areas covered by glaciers and underlain by permafrost

Kääb, Andreas

304

J. Phyr. A: Math. Gen. 24 (1991) 4129-4153. Printed in the UK A transfer-matrix Monte Carlo study of random  

E-print Network

J. Phyr. A: Math. Gen. 24 (1991) 4129-4153. Printed in the UK A transfer-matrix Monte Carlo study by the 36'and 72'rhombi. Applying the transfer matrix Monte Carla (TMMC) method to random tilings the three stiffness constants in the phason elasticity, one of which is not measurable by previous

Henley, Christopher L.

305

Prototeius stageri, Gen. et sp. Nov., a New Teiid Lizard from the Upper Cretaceous Marshalltown Formation of New Jersey, with a Preliminary Phylogenetic Revision of the Teiidae  

Microsoft Academic Search

A new fossil teiid lizard from the Upper Cretaceous Marshalltown Formation (Campanian) of Monmouth County, New Jersey is described as Prototeius stageri, gen. et sp. nov. Based on the holotypic dentary and referred specimens, the genus is diagnosed by a strongly differentiated heterodont dentition, five premaxillary teeth, paired frontals with well developed crista cranii, and a broad, low sagittal crest

Robert K. Denton Jr; Robert C. ONeill

1995-01-01

306

Appl Nbr Full TiFirst Name Middle Name Last Name Sex Category PH Category 00036777 F ADITI GUPTA F GEN N  

E-print Network

Appl Nbr Full TiFirst Name Middle Name Last Name Sex Category PH Category 00036777 F ADITI GUPTA F 00036674 F SRISHTI VIVEK SHARMA F GEN N Appl Nbr Full TiFirst Name Middle Name Last Name Sex Category PH) Appl Nbr Full TiFirst Name Middle Name Last Name Sex Category PH Category 00032299 F SANDEEP KUMAR

Ribeiro, Vinay

307

Stages in the Development of Choriopsoropts Kenyensis Gen. et Sp. N. (Acari: Sarcoptiformes: Psoroptidae), A Body Mange Mite from Captive African Buffalo, Syncerus Caffer, in Kenya.  

National Technical Information Service (NTIS)

Stages in the life cycle of Choriopsoroptes kenyensis gen. et. sp. n. are described. The stages for both sexes consist of the egg, larva, protonymph, triponymph, and adult, with the last 3 showing sexual dimorphism. The adult male forms an attachment pair...

G. K. Sweatman, J. A. Bindernagel, J. B. Walker

1971-01-01

308

Human GEN1 and the SLX4-associated nucleases MUS81 and SLX1 are essential for the resolution of replication-induced Holliday junctions  

PubMed Central

Summary Holliday junctions (HJs), the DNA intermediates of homologous recombination need to be faithfully processed in order to preserve genome integrity. In human cells the BLM helicase complex promotes non-nucleolytic dissolution of double HJs. In vitro, HJs may be nucleolytically processed by MUS81-EME1, GEN1, and SLX4-SLX1. Here, we exploit human SLX4-null cells to examine the requirements for HJ resolution in vivo. Lack of BLM and SLX4 or GEN1 and SLX4 are synthetically lethal in the absence of exogenous DNA damage with lethality being a consequence of dysfunctional mitosis proceeding in the presence of unprocessed HJs. Thus, GEN1 activity cannot substitute for the SLX4-associated nucleases and one of the HJ resolvase activities, either those associated with SLX4 or GEN1 is required for cell viability even in the presence of BLM. In-vivo HJ resolution depends on both SLX4-associated MUS81-EME1 and SLX1, suggesting that they are acting in concert in the context of SLX4. PMID:24080495

Garner, Elizabeth; Kim, Yonghwan; Lach, Francis P.; Kottemann, Molly C.; Smogorzewska, Agata

2013-01-01

309

Ligabuesaurus leanzai gen. et sp. nov. (Dinosauria, Sauropoda), a new titanosaur from the Lohan Cura Formation (Aptian, Lower Cretaceous) of Neuquén, Patagonia, Argentina  

Microsoft Academic Search

Ligabuesaurus leanzai gen. et sp. nov. is a new titanosaur (Saurischia, Sauropoda) from the Lower Cretaceous of Neuquén Basin, north Patagonia, Argentina. The fossil remains were found in the upper section of the Lohan Cura Formation, which is regarded as Late Aptian–Albian in age. Remains include an incomplete maxilla with ten teeth, six cervical and dorsal vertebrae, and several associated

José F. Bonaparte; Bernardo J. González Riga; Sebastián Apesteguía

2006-01-01

310

Omemeea maxbassiensis n. gen., n. sp. (Nematoda: Aphelenchoididae) from Galleries of the Bark Beetle Lepersinus californicus Sw. (Coleoptera: Scolytidae) in North Dakota  

PubMed Central

Omemeea maxbassiensis n. gen., n. sp. was found inhabiting galleries of a bark beetle, Lepersinus californicus Sw., in green ash, Fraxinus pennsylvanica Marsh. The genus differs from all other genera in the subfamily in its uniquely shaped umbrella-like head, distinctive stylet, and location of excretory pore. PMID:19322384

Massey, C. L.

1971-01-01

311

Omemeea maxbassiensis n. gen., n. sp. (Nematoda: Aphelenchoididae) from Galleries of the Bark Beetle Lepersinus californicus Sw. (Coleoptera: Scolytidae) in North Dakota.  

PubMed

Omemeea maxbassiensis n. gen., n. sp. was found inhabiting galleries of a bark beetle, Lepersinus californicus Sw., in green ash, Fraxinus pennsylvanica Marsh. The genus differs from all other genera in the subfamily in its uniquely shaped umbrella-like head, distinctive stylet, and location of excretory pore. PMID:19322384

Massey, C L

1971-07-01

312

Amorosia littoralis gen. sp. nov., a new genus and species name for the scorpinone and caffeine-producing hyphomycete from the littoral zone in The Bahamas  

Microsoft Academic Search

The new generic and species name Amorosia littoralis gen. sp. nov. is introduced for the conidial dematiaceous hyphomycete isolated from the littoral zone in The Bahamas and reported in 2001 to produce the novel aza-anthraquinone scorpinone, and also caffeine. No satisfactory generic placement was found at the time, but subsequent morphological and molecular investigations reveal that a new generic name

Peter G. Mantle; David L. Hawksworth; Sylvie Pazoutova; Lucy M. Collinson; Birgitte R. Rassing

2006-01-01

313

Session K--Estimating Forest Fuels--Gebert, Schuster, Woudenberg, O'Brien USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 285  

E-print Network

million tons) of total forest biomass. Additionally, we estimate that around 57 percent (619 million tons) of the estimated 1.08 billion tons of biomass is found on high fire-risk forest lands. Of these 619 million tonsSession K--Estimating Forest Fuels--Gebert, Schuster, Woudenberg, O'Brien USDA Forest Service Gen

Standiford, Richard B.

314

Session B--Estimating Forest Fuels--Gebert, Schuster, Woudenberg, O'Brien USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008 39  

E-print Network

million tons) of total forest biomass. Additionally, we estimate that around 57 percent (619 million tons) of the estimated 1.08 billion tons of biomass is found on high fire- risk forest lands. Of these 619 million tonsSession B--Estimating Forest Fuels--Gebert, Schuster, Woudenberg, O'Brien USDA Forest Service Gen

Standiford, Richard B.

315

Poster Session--Predicting Patterns of Alien Plant Invasion--Underwood, Klinger, Moore USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 361  

E-print Network

Poster Session--Predicting Patterns of Alien Plant Invasion--Underwood, Klinger, Moore USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 361 Predicting Patterns of Alien Plant Invasions in Areas of alien plant species. This is particularly problematic in areas which have experienced disturbances

Standiford, Richard B.

316

Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces.  

PubMed

During attempts to obtain novel, human-associated species of the domain Archaea, a coccoid micro-organism, designated strain B10(T), was isolated in pure culture from a sample of human faeces collected in Marseille, France. On the basis of its phenotypic characteristics and 16S rRNA and mcrA gene sequences, the novel strain was classified as a methanogenic archaeon. Cells of the strain were non-motile, Gram-staining-positive cocci that were approximately 850 nm in diameter and showed autofluorescence at 420 nm. Cells were lysed by 0.1% (w/v) SDS. With hydrogen as the electron donor, strain B10(T) produced methane by reducing methanol. The novel strain was unable to produce methane when hydrogen or methanol was the sole energy source. In an atmosphere containing CO(2), strain B10(T) could not produce methane from formate, acetate, trimethylamine, 2-butanol, 2-propanol, cyclopentanol, 2-pentanol, ethanol, 1-propanol or 2,3-butanediol. Strain B10(T) grew optimally with 0.5-1.0% (w/v) NaCl, at pH 7.6 and at 37 °C. It required tungstate-selenite for growth. The complete genome of the novel strain was sequenced; the size of the genome was estimated to be 2.05 Mb and the genomic DNA G+C content was 59.93 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, the highest sequence similarities (98.0-98.7%) were seen between strain B10(T) and several uncultured, methanogenic Archaea that had been collected from the digestive tracts of a cockroach, a chicken and mammals. In the same analysis, the non-methanogenic 'Candidatus Aciduliprofundum boonei' DSM 19572 was identified as the cultured micro-organism that was most closely related to strain B10(T) (83.0% 16S rRNA gene sequence similarity). Each of the three treeing algorithms used in the analysis of 16S rRNA gene sequences indicated that strain B10(T) belongs to a novel order that is distinct from the Thermoplasmatales. The novel strain also appeared to be distinct from Methanosphaera stadtmanae DSM 3091(T) (72.9% 16S rRNA gene sequence similarity), another methanogenic archaeon that was isolated from human faeces and can use methanol in the presence of hydrogen. Based on the genetic and phenotypic evidence, strain B10(T) represents a novel species of a new genus for which the name Methanomassiliicoccus luminyensis gen. nov., sp. nov. is proposed. The type strain of the type species is B10(T) (?=?DSM 24529(T)?=?CSUR P135(T)). PMID:22859731

Dridi, Bédis; Fardeau, Marie-Laure; Ollivier, Bernard; Raoult, Didier; Drancourt, Michel

2012-08-01

317

Progress reports for Gen IV sodium fast reactor activities FY 2007.  

SciTech Connect

An important goal of the US DOE Sodium Fast Reactor (SFR) program is to develop the technology necessary to increase safety margins in future fast reactor systems. Although no decision has been made yet about who will build the next demonstration fast reactor, it seems likely that the construction team will include a combination of international companies, and the safety design philosophy for the reactor will reflect a consensus of the participating countries. A significant amount of experience in the design and safety analysis of Sodium Fast Reactors (SFR) using oxide fuel has been developed in both Japan and France during last few decades. In the US, the traditional approach to reactor safety is based on the principle of defense-in-depth, which is usually expressed in physical terms as multiple barriers to release of radioactive material (e.g. cladding, reactor vessel, containment building), but it is understood that the 'barriers' may consist of active systems or even procedures. As implemented in a reactor design, defense-in-depth is classed in levels of safety. Level 1 includes measures to specify and build a reliable design with significant safety margins that will perform according to the intentions of the designers. Level 2 consists of additional design measures, usually active systems, to protect against unlikely accidental events that may occur during the life of the plant. Level 3 design measures are intended to protect the public in the event of an extremely unlikely accident not foreseen to occur during the plant's life. All of the design measures that make up the first three levels of safety are within the design basis of the plant. Beyond Level 3, and beyond the normal design basis, there are accidents that are not expected to occur in a whole generation of plants, and it is in this class that severe accidents, i.e. accidents involving core melting, are included. Beyond design basis measures to address severe accidents are usually identified as being for prevention of progression into severe accident conditions (prevention of core melting) or for mitigation of severe accident consequences (mitigation of the impact of core melting to protect public health and safety). Because design measures for severe accident prevention and mitigation are beyond the normal design basis, established regulatory guidelines and codes do not provide explicit identification of the design performance requirements for severe accident accommodation. The treatment of severe accidents is one of the key issues of R&D plans for the Gen IV systems in general, and for the Sodium Fast Reactor (SFR) in particular. Despite the lack of an unambiguous definition of safety approach applicable for severe accidents, there is an emerging consensus on the need for their consideration for the design. The US SFR program and Argonne National Laboratory (ANL) in particular have actively studied the potential scenarios and consequences of Hypothetical Core Disruptive Accidents (HCDA) for SFRs with oxide fuel during the Fast Flux Test Facility (FFTF) and Clinch River Breeder Reactor Plant (CRBRP) programs in the 70s and 80s. Later, the focus of the US SFR safety R&D activities shifted to the prevention of all HCDAs through passive safety features of the SFRs with metal fuel in the Integral Fast Reactor (IFR) program, and the study of severe accident consequences was de-emphasized. The goal of this paper is to provide an overview of the current SFR safety approach and the role of severe accidents in Japan and France, in preparation for an expected and more active collaboration in this area between the US, Japan, and France.

Cahalan, J. E.; Tentner, A. M.; Nuclear Engineering Division

2007-10-04

318

Trilosporoides platessae gen. et sp. n. (Myxozoa: Multivalvulida) in the plaice Pleuronectes platessa (Teleostei: Pleuronectidae) from Denmark.  

PubMed

A new myxosporean species, Trilosporoides platessae gen. et sp. n. (Multivalvulida), is described from the gallbladder of the plaice Pleuronectes platessa L. (Pleuronectidae) from Denmark. The myxospore of T. platessae is conical in side view, with a 24 microm long, pointed posterior projection. In apical view, the myxospore (diameter 9.4 microm) is round, trilobed and with three spherical polar capsules arranged peripherally, equidistant and opening peripherally through protruding tips. The polar capsules are of different sizes, one often larger than the others (diameter 3.3 microm vs. 2.5 microm). Apart from the long posterior projection, the myxospore of T. platessae differs from those of the three known species of Trilospora Noble, 1959 and from all genera within the order Multivalvulida Shulman, 1959 in the arrangement of the polar capsules. Trilosporoides platessae may temporarily be placed in the vicinity of the Trilosporidae. PMID:16405293

Køie, Marianne

2005-11-01

319

The description of Paralongicollum nemacheili n. gen., n. sp. (Acanthocephala: Pomphorhynchidae) from freshwater fishes in Kazakh S.S.R.  

PubMed

Paralongicollum nemacheili n. gen., n. sp. is described from Salmo gairdneri Richardson and Nemacheilus stoliczkai Steindacher in Lake Kul'say in the basin of Lake Balkhash, Kazakh S.S.R. Its long uniformly cylindrical neck and nonfiliform proboscis distinguish it from the other 3 genera of the family. Tenuiproboscis Yamaguti, 1935, has a filiform proboscis. The neck of Pomphorhynchus Monticelli, 1905, has a bulb anteriorly, and that of Longicollum Yamaguti, 1935, is spirally twisted with expansions. A key to the genera of Pomphorhynchidae is provided. The relatively longer necks in juveniles than in larger worms probably enhance the establishment of new infections. A large proportion of worms had extensive body wall deformities. Longicollum sergenti (Choquette and Gayot, 1952) Golvan, 1969, is relegated to the new genus Paralongicollum. PMID:1992092

Amin, O M; Bauer, O N; Sidorov, E G

1991-02-01

320

Third-Party Evaluation of Petro Tex Hydrocarbons, LLC, ReGen Lubricating Oil Re-refining Process  

SciTech Connect

This report presents an assessment of market, energy impact, and utility of the PetroTex Hydrocarbons, LLC., ReGen process for re-refining used lubricating oil to produce Group I, II, and III base oils, diesel fuel, and asphalt. PetroTex Hydrocarbons, LLC., has performed extensive pilot scale evaluations, computer simulations, and market studies of this process and is presently evaluating construction of a 23 million gallon per year industrial-scale plant. PetroTex has obtained a 30 acre site in the Texas Industries RailPark in Midlothian Texas. The environmental and civil engineering assessments of the site are completed, and the company has been granted a special use permit from the City of Midlothian and air emissions permits for the Texas Commission on Environmental Quality.

Compere, A L [ORNL; Griffith, William {Bill} L [ORNL

2009-04-01

321

Characterization of Some Actinomyces-Like Isolates from Human Clinical Sources: Description of Varibaculum cambriensis gen. nov., sp. nov.  

PubMed Central

Fifteen strains of an anaerobic, catalase-negative, gram-positive diphtheroid-shaped bacterium recovered from human sources were characterized by phenotypic and molecular chemical and molecular genetic methods. The unidentified bacterium showed some resemblance to Actinomyces species and related taxa, but biochemical testing, polyacrylamide gel electrophoresis analysis of whole-cell proteins, and amplified 16S ribosomal DNA restriction analysis indicated the strains were distinct from all currently named Actinomyces species and related taxa. Comparative 16S rRNA gene sequencing studies showed that the bacterium represents a hitherto-unknown phylogenetic line that is related to but distinct from Actinomyces, Actinobaculum, Arcanobacterium, and Mobiluncus. We propose, on the basis of phenotypic and phylogenetic evidence, that the unknown bacterium from human clinical specimens should be classified as a new genus and species, Varibaculum cambriensis gen. nov., sp. nov. The type strain of Varibaculum cambriensis sp. nov. is CCUG 44998T = CIP 107344T. PMID:12574260

Hall, Val; Collins, Matthew D.; Lawson, Paul A.; Hutson, Roger A.; Falsen, Enevold; Inganas, Elisabeth; Duerden, Brian

2003-01-01

322

Experimental Investigations of the Ablation of Wire Arrays on the 250 kA GenASIS Machine  

NASA Astrophysics Data System (ADS)

We present investigations of exploding wire experiments on a recently completed linear transformer driver (LTD) in the High Energy Density Physics laboratory at UCSD. The GenASIS machine delivers >250kA in 130ns to short circuit and >200kA to a wire array load, via a conical constant gap power feed. Measured load currents compare favorably to circuit modeling. This new generator facilitates ablation studies of multiple wire cylindrical arrays with >25 kA/ wire, and we present laser Schlieren imaging, along with radial and axial electron density profiles inferred from interferometry for Al and W arrays, which are compared to analytical theory. In addition, conical wire arrays are used to generate supersonic plasma jets. We present characterization of high atomic number jets along with estimates of the local sound speed and Mach number.

Bott, S. C.; Haas, D. M.; Eshaq, Y.; Ueda, U.; Madden, R. E.; Collins, G.; Beg, F. N.

2008-11-01

323

Advenella incenata gen. nov., sp. nov., a novel member of the Alcaligenaceae, isolated from various clinical samples.  

PubMed

A polyphasic taxonomic study of 14 isolates recovered from various human and veterinary clinical samples was performed. Phenotypically these isolates shared several characteristics with members of the Alcaligenaceae and related genera. Random amplified polymorphic DNA fingerprinting and whole-cell protein analysis suggested the presence of multiple genomic groups, which was confirmed by DNA-DNA hybridization experiments. 16S rRNA gene sequence analysis indicated that these isolates were related to the genera Pelistega, Taylorella, Oligella, Pigmentiphaga, Alcaligenes, Kerstersia, Achromobacter and Bordetella and belonged to the family Alcaligenaceae. Based on the results of the present study the organisms were classified in a novel genus, Advenella gen. nov. This genus comprises one named species, Advenella incenata sp. nov. (type strain LMG 22250T=CCUG 45225T) and five currently unnamed genomic species. The DNA G+C content of members of the novel genus Advenella is between 54.0 and 57.7 mol%. PMID:15653883

Coenye, Tom; Vanlaere, Elke; Samyn, Emly; Falsen, Enevold; Larsson, Peter; Vandamme, Peter

2005-01-01

324

A new genus of Strepsiptera, Rozenia gen. n. (Stylopidae), a parasite of bee genera Acamptopoeum and Calliopsis (Andrenidae, Panurginae, Calliopsini)  

PubMed Central

Abstract A new Strepsiptera genus from South America is described, Rozenia gen. n., with three new species: Rozenia calliopsidis sp. n. (type species), Rozenia peruana sp. n. and Rozenia platicephala sp. n. These three new species are parasites of bees belonging to the tribe Calliopsini (Andrenidae, Panurginae). Rozenia calliopsidis sp. n. is a parasite of the bee genus Calliopsis Smith, 1853 and Rozenia peruana sp. n. and Rozenia platicephala sp. n. are parasites of the bee genus Acamptopoeum Cockerell, 1905. Diagnoses and descriptions of female puparia are presented for all three species. Diagnoses and descriptions of first instars (triungulinids) are presented for Rozenia calliopsidis sp. n. and Rozenia platicephala sp. n. The first case of increased number of setae on the body of the first instars and augmentation of chaetotaxy of Strepsiptera are discussed. PMID:25349488

Straka, Jakub; J?zová, Katerina; Batelka, Jan

2014-01-01

325

Haootia quadriformis n. gen., n. sp., interpreted as a muscular cnidarian impression from the Late Ediacaran period (approx. 560 Ma).  

PubMed

Muscle tissue is a fundamentally eumetazoan attribute. The oldest evidence for fossilized muscular tissue before the Early Cambrian has hitherto remained moot, being reliant upon indirect evidence in the form of Late Ediacaran ichnofossils. We here report a candidate muscle-bearing organism, Haootia quadriformis n. gen., n. sp., from approximately 560 Ma strata in Newfoundland, Canada. This taxon exhibits sediment moulds of twisted, superimposed fibrous bundles arranged quadrilaterally, extending into four prominent bifurcating corner branches. Haootia is distinct from all previously published contemporaneous Ediacaran macrofossils in its symmetrically fibrous, rather than frondose, architecture. Its bundled fibres, morphology, and taphonomy compare well with the muscle fibres of fossil and extant Cnidaria, particularly the benthic Staurozoa. Haootia quadriformis thus potentially provides the earliest body fossil evidence for both metazoan musculature, and for Eumetazoa, in the geological record. PMID:25165764

Liu, Alexander G; Matthews, Jack J; Menon, Latha R; McIlroy, Duncan; Brasier, Martin D

2014-10-22

326

Haootia quadriformis n. gen., n. sp., interpreted as a muscular cnidarian impression from the Late Ediacaran period (approx. 560 Ma)  

PubMed Central

Muscle tissue is a fundamentally eumetazoan attribute. The oldest evidence for fossilized muscular tissue before the Early Cambrian has hitherto remained moot, being reliant upon indirect evidence in the form of Late Ediacaran ichnofossils. We here report a candidate muscle-bearing organism, Haootia quadriformis n. gen., n. sp., from approximately 560 Ma strata in Newfoundland, Canada. This taxon exhibits sediment moulds of twisted, superimposed fibrous bundles arranged quadrilaterally, extending into four prominent bifurcating corner branches. Haootia is distinct from all previously published contemporaneous Ediacaran macrofossils in its symmetrically fibrous, rather than frondose, architecture. Its bundled fibres, morphology, and taphonomy compare well with the muscle fibres of fossil and extant Cnidaria, particularly the benthic Staurozoa. Haootia quadriformis thus potentially provides the earliest body fossil evidence for both metazoan musculature, and for Eumetazoa, in the geological record. PMID:25165764

Liu, Alexander G.; Matthews, Jack J.; Menon, Latha R.; McIlroy, Duncan; Brasier, Martin D.

2014-01-01

327

Evaluating the Suitability for CO2 Storage at the FutureGen 2.0 Site, Morgan County, Illinois, USA  

SciTech Connect

FutureGen 2.0 site will be the first near-zero emission power plant with fully integrated long-term storage in a deep, non-potable saline aquifer in the United States. The proposed FutureGen 2.0 CO2 storage site is located in northeast Morgan County, Illinois, U.S.A., forty-eight kilometres from the Meredosia Energy Center where a large-scale oxy-combustion demonstration will be conducted. The demonstration will involve > 90% carbon capture, which will produce more than one million metric tons (MMT) of CO2 per year. The CO2 will be compressed at the power plant and transported via pipeline to the storage site. To examine CO2 storage potential of the site, a 1,467m characterization well (FGA#1) was completed in December 2011. The target reservoir for CO2 storage is the Mt. Simon Sandstone and Elmhurst Sandstone Member of the lower Eau Claire Formation for a combined thickness of 176 m. Confining beds of the overlying Lombard and Proviso Members (upper Eau Claire Formation) reach a thickness of 126 m. Characterization of the target injection zone and the overlying confining zone was based on wellbore data, cores, and geophysical logs, along with surface geophysical (2-D seismic profiles, magnetic and gravity), and structural data collected during the initial stage of the project . Based on this geological model, 3D simulations of CO2 injection and redistribution were conducted using STOMP-CO2, a multiphase flow and transport simulator. After this characterization stage, it appears that the injection site is a suitable geologic system for CO2 sequestration and that the injection zone is sufficient to receive up to 33 MMT of CO2 at a rate of 1.1 MMT/yr. GHGT-11 conference

Bonneville, Alain; Gilmore, Tyler J.; Sullivan, E. C.; Vermeul, Vincent R.; Kelley, Mark E.; White, Signe K.; Appriou, Delphine; Bjornstad, Bruce N.; Gerst, Jacqueline L.; Gupta, Neeraj; Horner, Jacob A.; McNeil, Caitlin; Moody, Mark A.; Rike, William M.; Spane, Frank A.; Thorne, Paul D.; Zeller, Evan R.; Zhang, Z. F.; Hoffman, Jeffrey; Humphreys, Kenneth K.

2013-08-05

328

Draconibacterium orientale gen. nov., sp. nov., isolated from two distinct marine environments, and proposal of Draconibacteriaceae fam. nov.  

PubMed

The taxonomic characteristics of two bacterial strains, FH5T and SS4, isolated from enrichment cultures obtained from two distinct marine environments, were determined. These bacteria were Gram-stain-negative, facultatively anaerobic rods. Growth occurred at 20-40 °C (optimum, 28-32 °C), pH 5.5-9.0 (optimum, pH 7.0-7.5) and in the presence of 1-7% NaCl (optimum, 2-4%). The major cellular fatty acids were anteiso-C15:0 and iso-C15:0. Menaquinone 7 (MK-7) was the sole respiratory quinone. The major polar lipids were phosphatidylethanolamine, an unkown phospholipid and an unknown lipid. The DNA G+C contents of strains FH5T and SS4 were both determined to be 42.0?mol%. The results of DNA-DNA hybridization studies indicated that the FH5T and SS4 genomes share greater than 95% relatedness. The strains formed a distinct phyletic line within the class Bacteroidia, with less than 89.4% sequence similarity to their closest relatives with validly published names. On the basis of physiological and biochemical characteristics, 16S rRNA gene sequences and chemical properties, a novel genus and species, Draconibacterium orientale gen. nov., sp. nov., within the class Bacteroidia, are proposed, with strain FH5T (=DSM 25947T=CICC 10585T) as the type strain. In addition, a new family, Draconibacteriaceae fam. nov., is proposed to accommodate Draconibacterium gen. nov. PMID:24523447

Du, Zong-Jun; Wang, Ying; Dunlap, Christopher; Rooney, Alejandro P; Chen, Guan-Jun

2014-05-01

329

Paukš?iuose aptinkam? neapib?dint? Sarcocystis genties r?ši? filogenetini? ryši? tyrimas naudojant dalines 18S ir 28S rRNR gen? sekas.  

E-print Network

??SANTRAUKA PAUKŠ?IUOSE APTINKAM? NEAPIB?DINT? SARCOCYSTIS GENTIES R?ŠI? FILOGENETINI? RYŠI? TYRIMAS NAUDOJANT DALINES 18S IR 28S rRNR GEN? SEKAS Petras Prakas Vilniaus Universiteto Ekologijos Institutas, Populiacin?s… (more)

Prakas,; Petras

2009-01-01

330

Molecular Identification of Hydroxylysine Kinase and of Ammoniophospholyases Acting on 5-Phosphohydroxy-l-lysine and Phosphoethanolamine*  

PubMed Central

The purpose of the present work was to identify the catalytic activity of AGXT2L1 and AGXT2L2, two closely related, putative pyridoxal-phosphate-dependent enzymes encoded by vertebrate genomes. The existence of bacterial homologues (40–50% identity with AGXT2L1 and AGXT2L2) forming bi- or tri-functional proteins with a putative kinase belonging to the family of aminoglycoside phosphotransferases suggested that AGXT2L1 and AGXT2L2 acted on phosphorylated and aminated compounds. Vertebrate genomes were found to encode a homologue (AGPHD1) of these putative bacterial kinases, which was therefore likely to phosphorylate an amino compound bearing a hydroxyl group. These and other considerations led us to hypothesize that AGPHD1 corresponded to 5-hydroxy-l-lysine kinase and that AGXT2L1 and AGXT2L2 catalyzed the pyridoxal-phosphate-dependent breakdown of phosphoethanolamine and 5-phosphohydroxy-l-lysine. The three recombinant human proteins were produced and purified to homogeneity. AGPHD1 was indeed found to catalyze the GTP-dependent phosphorylation of 5-hydroxy-l-lysine. The phosphorylation product made by this enzyme was metabolized by AGXT2L2, which converted it to ammonia, inorganic phosphate, and 2-aminoadipate semialdehyde. AGXT2L1 catalyzed a similar reaction on phosphoethanolamine, converting it to ammonia, inorganic phosphate, and acetaldehyde. AGPHD1 and AGXT2L2 are likely to be the mutated enzymes in 5-hydroxylysinuria and 5-phosphohydroxylysinuria, respectively. The high level of expression of AGXT2L1 in human brain, as well as data in the literature linking AGXT2L1 to schizophrenia and bipolar disorders, suggest that these diseases may involve a perturbation of brain phosphoethanolamine metabolism. AGXT2L1 and AGXT2L2, the first ammoniophospholyases to be identified, belong to a family of aminotransferases acting on ?-amines. PMID:22241472

Veiga-da-Cunha, Maria; Hadi, Farah; Balligand, Thomas; Stroobant, Vincent; Van Schaftingen, Emile

2012-01-01

331

Boltimys broomi gen. nov., sp. nov. (Rodentia, Mammalia), nouveau Muridae d'affinité incertaine du Pliocène inférieur d'Afrique du Sud  

NASA Astrophysics Data System (ADS)

Boltimys broomi gen. nov., sp. nov., a Muridae of uncertain affinity in the Early Pliocene of South Africa. Boltimys broomi gen. nov., sp. nov. is reported from the Early Pliocene fauna of Waypoint 160, a fossiliferous locality in the area of Bolt's Farm (Province of Gauteng) near Krugersdorp in South Africa. The occlusal surface of the jugal teeth is characterized by a basin-shaped aspect due to the coalescence of the cusps which make the lobes of the molars. An accessory inner cusp is present on the first and second upper molars. A faint longitudinal crest is present only in the first lower molar. The new rodent is tentatively referred to the subfamily Myocricetodontinae.

Sénégas, Frank; Michaux, Jacques

2000-04-01

332

A new remarkable subterranean beetle of the Rhodopes: Paralovricia gen. n. beroni sp. n. belonging to Lovriciina new subtribe (Coleoptera, Carabidae, Trechinae, Bembidiini)  

PubMed Central

Abstract Paralovricia gen. n. beroni sp. n., belonging to the new subtribe Lovriciina, is described from two caves in the Western Rhodopes (Bulgaria): Kraypatnata peshtera, near Smilyan Village (Smolyan Municipality) and Snezhanka, near Peshtera Town (Peshtera Municipality). Three currently known genera, Lovricia Pretner, 1979, Neolovricia Lakota, Jalži? & Moravec, 2009 and Paralovricia gen. n. represent a monophyletic unit supported by important synapomorphies that allows to propose the establishment of the new subtribe Lovriciina, characterized by the following characters: last maxillary palpomeres very long and narrow, basal angles of pronotum without seta, elytra without discal setae, elytral umbilicate series of nine pores in which the main pores are the 2nd, 6th and 9th, apical recurrent striole absent and mesotibial apex expanded outward. Its systematic position within the subfamily Trechinae (sensu Lorenz 2005) is discussed and Lovriciina is placed near Anillina. Key to the genera of the subtribe is proposed. Distribution data and zoogeographical hypotheses are discussed. PMID:21998506

Giachino, Pier Mauro; Gueorguiev, Borislav; Vailati, Dante

2011-01-01

333

Non contiguous-finished genome sequence and description of Dielma fastidiosa gen. nov., sp. nov., a new member of the Family Erysipelotrichaceae  

PubMed Central

Dielma fastidiosa strain JC13T gen. nov., sp. nov. is the type strain of D. fastidiosa gen. nov., sp. nov., the type species of a new genus within the family Erysipelotrichaceae. This strain, whose draft genome is described here, was isolated from the fecal flora of a healthy 16-year-old male Senegalese volunteer. D. fastidiosa is a Gram-negative anaerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,574,031 bp long genome comprises a 3,556,241-bp chromosome and a 17,790-bp plasmid. The chromosome contains 3,441 protein-coding and 50 RNA genes, including 3 rRNA genes, whereas the plasmid contains 17 protein-coding genes. PMID:23991263

Ramasamy, Dhamodharan; Lagier, Jean-Christophe; Nguyen, Thi Tien; Raoult, Didier; Fournier, Pierre-Edouard

2013-01-01

334

Dentirumai philippinensis n. gen., n. sp. (Nematoda: Philometridae), a new tissue-infecting philometrid nematode from the loach goby Rhyacichthys aspro (Valenciennes) (Rhyacichthyidae) in the Philippines.  

PubMed

A new genus and species of the philometrid nematode Dentirumai philippinensis n. gen., n. sp. Philometrinae, Philometridae, are described on the basis of the female specimens found in the loach goby, Rhyacichthys aspro (Valenciennes), from the upper Bianuan River, Municipality of Casiguran, Aurora Province, in the Philippine Archipelago. Dentirumai philippinensis was collected from the body cavity, subcutaneous tissues near the bases of the pectoral and pelvic fins, and surrounding body tissues in the hypaxial musculature of R. aspro. Based on light microscopic and scanning electron microscopic examination, the new nematode species is morphologically close to the genus Rumai Travassos, 1960 except for one major difference, i.e. the presence of a sclerotized ring in the oral aperture armed with distinct numerous minute teeth on its inner surface. This important taxonomic feature makes it possible to erect a new genus, Dentirumai n. gen. to accommodate the newly discovered philometrid species. A key to genera of the Philometrinae is provided. PMID:22293391

Quiazon, K M A; Moravec, F

2013-03-01

335

Alcalilimnicola halodurans gen. nov., sp. nov., an alkaliphilic, moderately halophilic and extremely halotolerant bacterium, isolated from sediments of soda-depositing Lake Natron, East Africa Rift Valley  

Microsoft Academic Search

concentrations of 0-28% (w\\/v), with optimal growth at 3-8% (w\\/v) NaCl. The bacterium preferentially metabolized volatile fatty acids and required vitamins for growth. The name Alcalilimnicola halodurans gen. nov., sp. nov. is proposed for the novel isolate, placed in the c-Proteobacteria within the family Ectothiorhodospiraceae on the basis of analysis of the 16S rDNA sequence, polar lipids, fatty acids and

Michail M. Yakimov; Laura Giuliano; Tatiana N. Chernikova; Gabriella Gentile; Wolf-Rainer Abraham; Heinrich Lu; Kenneth N. Timmis; Peter N. Golyshin

336

Wood-inhabiting freshwater fungi from Thailand: Ascothailandia grenadoidia gen. et sp. nov., Canalisporium grenadoidia sp. nov. with a key to Canalisporium species (Sordariomycetes, Ascomycota)  

Microsoft Academic Search

Ascothailandia grenadoidia gen. et sp. nov. is described and illustrated from submerged wood (Wrightia tomentosa) in a stream at Hala Bala Wildlife Sanctuary, southern Thailand. The new genus (teleomorph) is characterized by perithecoid,\\u000a globose, dark brown, ostiolate ascomata, paraphysate, asci cylindrical, unitunicate with a prominent J-refractive apical ring\\u000a and versicolurus, 3-euseptate ascospores. Ascospores germinated producing a Canalisporium (C. grenadoidia sp.

Veera Sri-indrasutdhi; Nattawut Boonyuen; Satinee Suetrong; Charuwan Chuaseeharonnachai; Somsak Sivichai; E. B. Gareth Jones

2010-01-01

337

CSU, FULLERTON CREDIT FOR EXTERNAL EXAMS (AP, IB, CLEP) ADVANCED PLACEMENT EXAMS (AP) SCORE UNITS COURSE CREDIT GEN EDUC BEGIN DATE END DATE  

E-print Network

) SCORE UNITS COURSE CREDIT GEN EDUC BEGIN DATE END DATE AP ITALIAN LANGUAGE & CULTURE 3-5 5 ITAL 101 GE CHINESE LANGUAGE & CULTURE 3-5 5 CHIN 101 GE III.B.2 5 CHIN 102 GE III.B.2 AP COMPUTER SCIENCE A 3-5 3 III.B.2 (Exam discontinued Fall 2009) 5 ITAL 102 GE III.B.2 AP JAPANESE LANGUAGE & CULTURE 3-5 5 JAPN

de Lijser, Peter

338

A new genus of oak gallwasp, Coffeikokkos Pujade-Villar & Melika, gen. n., with a description of a new species from Costa Rica (Hymenoptera, Cynipidae).  

PubMed

A new genus of oak gallwasp, Coffeikokkos Pujade-Villar & Melika, gen. n., is described from Costa Rica. Diagnostic characters and generic limits of the new genus are discussed in detail. The new genus includes Coffeikokkos copeyensis Pujade-Villar & Melika, sp. n., which induces galls on stems of Quercus bumelioides, an endemic oak to Costa Rica, Honduras and Panama. The new species and galls are described and illustrated. PMID:22423188

Pujade-Villar, Juli; Hanson, Paul; Melika, George

2012-01-01

339

A new genus of oak gallwasp, Coffeikokkos Pujade-Villar & Melika, gen. n., with a description of a new species from Costa Rica (Hymenoptera, Cynipidae)  

PubMed Central

Abstract A new genus of oak gallwasp, Coffeikokkos Pujade-Villar & Melika, gen. n., is described from Costa Rica. Diagnostic characters and generic limits of the new genus are discussed in detail. The new genus includes Coffeikokkos copeyensis Pujade-Villar & Melika, sp. n., which induces galls on stems of Quercus bumelioides, an endemic oak to Costa Rica, Honduras and Panama. The new species and galls are described and illustrated. PMID:22423188

Pujade-Villar, Juli; Hanson, Paul; Melika, George

2012-01-01

340

A new African soft scale genus, Pseudocribrolecanium gen. nov. (Hemiptera: Coccoidea: Coccidae), erected for two species, including the citrus pest P. andersoni (Newstead) comb. nov  

PubMed Central

A new African genus of soft scale insects, Pseudocribrolecanium gen. nov. is erected to accommodate Akermes colae Green & Laing and Cribrolecanium andersoni (Newstead). The adult females and first-instar nymphs of the two species are redescribed and illustrated. Taxonomic keys to separate the adult females and first-instar nymphs are provided. The affinity of Pseudocribrolecanium with the tribe Paralecaniini in the subfamily Coccinae is discussed. PMID:19537997

Kondo, Takumasa

2006-01-01

341

Sensitivity Studies for Extraction of G_E^n from Inclusive and Semi-inclusive Electron Scattering on Polarized 3He  

E-print Network

The processes \\vec{3He}(\\vec{e},e') and \\vec{3He}(\\vec{e},e'n) are theoretically analyzed with the aim to search for sensitivities in the electric form factor of the neutron, G_E^n. Faddeev calculations based on the high precision NN force AV18 and using consistent MEC's are employed. While the inclusive process is too insensitive, the semi-exclusive one appears promising.

J. Golak; W. Glockle; H. Kamada; H. Witala; R. Skibinski; A. Nogga

2001-10-24

342

Description of Niveispirillum fermenti gen. nov., sp. nov., isolated from a fermentor in Taiwan, transfer of Azospirillum irakense (1989) as Niveispirillum irakense comb. nov., and reclassification of Azospirillum amazonense (1983) as Nitrospirillum amazonense gen. nov.  

PubMed

A taxonomic study was carried out on a novel aerobic bacterial strain (designated CC-LY736(T)) isolated from a fermentor in Taiwan. Cells of strain CC-LY736(T) were Gram-stain negative, spiral-shaped and motile by means of a monopolar flagellum. Strain CC-LY736(T) shared the greatest degree of 16S rRNA gene sequence similarity to Azospirillum irakense DSM 11586(T) (97.2 %), Rhodocista centenaria JCM 21060(T) (96.3 %) and Rhodocista pekingensis JCM 11669(T) (96.1 %). The major fatty acids were C16:0, C16:1 ?5c, C19:0 cyclo ?8c, C18:1 ?7c/C18:1 ?6c, C16:0 3-OH and C18:1 2-OH. The predominant polar lipids included phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidyldimethylethanolamine and two unidentified glycolipids. The common major respiratory quinone was ubiquinone Q-10 and predominant polyamines were sym-homospermidine and putrescine. The DNA G+C content of strain CC-LY736(T) was 67.6 ± 0.1 mol %. During phylogenetic analysis, strain CC-LY736(T) formed a unique phyletic lineage associated with Rhodocista species. However, the combination of genetic, chemotaxonomic and physiological data clearly indicated that strain CC-LY736(T) was a novel representative of the family Rhodospirillaceae. Based on the polyphasic comparison, the name Niveispirillum fermenti gen. nov., sp. nov. is proposed; the type strain of the type species is CC-LY736(T) (= BCRC 80504(T) = LMG 27263(T)). In addition, the reclassifications of Azospirillum irakense as Niveispirillum irakense comb. nov. (type strain KBC1(T) = ATCC 51182(T) = BCRC 15764(T) = CIP 103311(T)), and Azospirillum amazonense as Nitrospirillum amazonense gen. nov., sp. nov. (type strain Am14(T) = ATCC 35119(T) = BCRC 14279(T) = DSM 3787(T)) are proposed based on the polyphasic taxonomic data obtained in this study. PMID:24771126

Lin, Shih-Yao; Hameed, Asif; Shen, Fo-Ting; Liu, You-Cheng; Hsu, Yi-Han; Shahina, Mariyam; Lai, Wei-An; Young, Chiu-Chung

2014-06-01

343

Results of Total Knee Arthroplasty with NexGen LPS-flex Implant Using Navigation System (Brain Lab): Results with a 5-year Follow-up  

PubMed Central

Purpose To evaluate the clinical and radiological results of patients that underwent total knee arthroplasty (TKA) with a NexGen LPS-Flex implant using a Navigation system (Brain Lab). Materials and Methods Between January 2001 and December 2005, 55 knees in 46 patients which used the NexGen LPS-Flex implant with a Navigation system (Brain Lab) for primary TKA were clinically and radiologically evaluated after a minimum follow-up of 5 years. Evaluation included preoperative and postoperative range of motion (ROM), Knee Society Score (KSS), tibio-femoral angle and postoperative complications. Results Knee ROM was increased from 118.9° preoperatively to 126.9° at the last follow up. In addition, the preoperative flexion contracture improved from 6.5° to 1.8° postoperatively. The mean KSS and functional score were improved from 59.8 and 51.2 to postoperative scores of 86.4 and 85.2 respectively. The rate of appearance of radiolucency in X-ray was 21.8%. One case of superficial skin infection and one case of aseptic loosening were noted as complications but, did not require a revision surgery. Conclusions TKA with NexGen LPS-Flex implant using Navigation system (Brain Lab) showed satisfactory improvement in pain and function, but more long term follow up will be needed to complete verification. PMID:23269958

Kang, Chul Hyung; Lee, Kyung Jae; Cho, Chul Hyun; Lee, Si Wook; Shin, Hong Kwan; Lee, Young Kook; Bae, Ji Suk

2012-01-01

344

A Network Pharmacology Approach to Determine Active Compounds and Action Mechanisms of Ge-Gen-Qin-Lian Decoction for Treatment of Type 2 Diabetes  

PubMed Central

Traditional Chinese medicine (TCM) herbal formulae can be valuable therapeutic strategies and drug discovery resources. However, the active ingredients and action mechanisms of most TCM formulae remain unclear. Therefore, the identification of potent ingredients and their actions is a major challenge in TCM research. In this study, we used a network pharmacology approach we previously developed to help determine the potential antidiabetic ingredients from the traditional Ge-Gen-Qin-Lian decoction (GGQLD) formula. We predicted the target profiles of all available GGQLD ingredients to infer the active ingredients by clustering the target profile of ingredients with FDA-approved antidiabetic drugs. We also applied network target analysis to evaluate the links between herbal ingredients and pharmacological actions to help explain the action mechanisms of GGQLD. According to the predicted results, we confirmed that a novel antidiabetic ingredient from Puerariae Lobatae radix (Ge-Gen), 4-Hydroxymephenytoin, increased the insulin secretion in RIN-5F cells and improved insulin resistance in 3T3-L1 adipocytes. The network pharmacology strategy used here provided a powerful means for identifying bioactive ingredients and mechanisms of action for TCM herbal formulae, including Ge-Gen-Qin-Lian decoction. PMID:24527048

Li, Huiying; Zhao, Linhua; Zhang, Bo; Jiang, Yuyu; Wang, Xu; Guo, Yun; Liu, Hongxing; Li, Shao; Tong, Xiaolin

2014-01-01

345

[The impact of gen polymorphism of subunits of receptors of thrombocytes GP IIb/IIIa on variation of indicators of thrombocyte hemostasis in obstetrics practice].  

PubMed

The article presents the results of study of the impact of gen polymorphism of subunits of receptors of thrombocytes GP Ilb/IIIa on variation of quantitative, functional and morphometric parameters of thrombocytes in 408 puerperae. The heterozygous variant of mutation was established in women with physiologically progress of pregnancy and delivery and in women with clinical manifestations of thrombophilia. The homozygous variant was established only in women with thrombophilia. The relationship is established between the presence of hetero- and homozygous mutations of gen of subunits of receptors of thrombocytes GP IIb/IIIa and inclination to hypercoagulation. This relationship manifests itself in increasing of degree of thrombocytes aggregation with all inductors and as well as in increasing of functional activity and appearance of young active cells, according morphometric analysis data. The application of computer morphometry of thrombocytes in the study made it possible to ascertain the activization of thrombocyte component of hemostasis in healthy women and availability of heterozygous mutation of gen of subunits of receptors of thrombocytes GP IIb/IIIa (PlA1/PlA2). PMID:22624463

Bondar', T P; Muratova, A Iu

2012-02-01

346

Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors  

PubMed Central

Background Microarray Comparative Genomic Hybridization (array CGH) provides a means to examine DNA copy number aberrations. Various platforms, brands and underlying technologies are available, facing the user with many choices regarding platform sensitivity and number, localization, and density distribution of probes. Results We evaluate three different platforms presenting different nature and arrangement of the probes: The Agilent Human Genome CGH Microarray 44 k, the ROMA/NimbleGen Representational Oligonucleotide Microarray 82 k, and the Illumina Human-1 Genotyping 109 k BeadChip, with Agilent being gene oriented, ROMA/NimbleGen being genome oriented, and Illumina being genotyping oriented. We investigated copy number changes in 20 human breast tumor samples representing different gene expression subclasses, using a suite of graphical and statistical methods designed to work across platforms. Despite substantial differences in the composition and spatial distribution of probes, the comparison revealed high overall concordance. Notably however, some short amplifications and deletions of potential biological importance were not detected by all platforms. Both correlation and cluster analysis indicate a somewhat higher similarity between ROMA/NimbleGen and Illumina than between Agilent and the other two platforms. The programs developed for the analysis are available from . Conclusion We conclude that platforms based on different technology principles reveal similar aberration patterns, although we observed some unique amplification or deletion peaks at various locations, only detected by one of the platforms. The correct platform choice for a particular study is dependent on whether the appointed research intention is gene, genome, or genotype oriented. PMID:18691401

Baumbusch, LO; Aar?e, J; Johansen, FE; Hicks, J; Sun, H; Bruhn, L; Gunderson, K; Naume, B; Kristensen, VN; Liest?l, K; B?rresen-Dale, A-L; Lingjaerde, OC

2008-01-01

347

AtGEN1 and AtSEND1, Two Paralogs in Arabidopsis, Possess Holliday Junction Resolvase Activity1[W][OPEN  

PubMed Central

Holliday junctions (HJs) are physical links between homologous DNA molecules that arise as central intermediary structures during homologous recombination and repair in meiotic and somatic cells. It is necessary for these structures to be resolved to ensure correct chromosome segregation and other functions. In eukaryotes, including plants, homologs of a gene called XPG-like endonuclease1 (GEN1) have been identified that process HJs in a manner analogous to the HJ resolvases of phages, archaea, and bacteria. Here, we report that Arabidopsis (Arabidopsis thaliana), a eukaryotic organism, has two functional GEN1 homologs instead of one. Like all known eukaryotic resolvases, AtGEN1 and Arabidopsis single-strand DNA endonuclease1 both belong to class IV of the Rad2/XPG family of nucleases. Their resolvase activity shares the characteristics of the Escherichia coli radiation and UV sensitive C paradigm for resolvases, which involves resolving HJs by symmetrically oriented incisions in two opposing strands. This leads to ligatable products without the need for further processing. The observation that the sequence context influences the cleavage by the enzymes can be interpreted as a hint for the existence of sequence specificity. The two Arabidopsis paralogs differ in their preferred sequences. The precise cleavage positions observed for the resolution of mobile nicked HJs suggest that these cleavage positions are determined by both the substrate structure and the sequence context at the junction point. PMID:25037209

Bauknecht, Markus; Kobbe, Daniela

2014-01-01

348

GenHtr: a tool for comparative assessment of genetic heterogeneity in microbial genomes generated by massive short-read sequencing  

PubMed Central

Background Microevolution is the study of short-term changes of alleles within a population and their effects on the phenotype of organisms. The result of the below-species-level evolution is heterogeneity, where populations consist of subpopulations with a large number of structural variations. Heterogeneity analysis is thus essential to our understanding of how selective and neutral forces shape bacterial populations over a short period of time. The Solexa Genome Analyzer, a next-generation sequencing platform, allows millions of short sequencing reads to be obtained with great accuracy, allowing for the ability to study the dynamics of the bacterial population at the whole genome level. The tool referred to as GenHtr was developed for genome-wide heterogeneity analysis. Results For particular bacterial strains, GenHtr relies on a set of Solexa short reads on given bacteria pathogens and their isogenic reference genome to identify heterogeneity sites, the chromosomal positions with multiple variants of genes in the bacterial population, and variations that occur in large gene families. GenHtr accomplishes this by building and comparatively analyzing genome-wide heterogeneity genotypes for both the newly sequenced genomes (using massive short-read sequencing) and their isogenic reference (using simulated data). As proof of the concept, this approach was applied to SRX007711, the Solexa sequencing data for a newly sequenced Staphylococcus aureus subsp. USA300 cell line, and demonstrated that it could predict such multiple variants. They include multiple variants of genes critical in pathogenesis, e.g. genes encoding a LysR family transcriptional regulator, 23 S ribosomal RNA, and DNA mismatch repair protein MutS. The heterogeneity results in non-synonymous and nonsense mutations, leading to truncated proteins for both LysR and MutS. Conclusion GenHtr was developed for genome-wide heterogeneity analysis. Although it is much more time-consuming when compared to Maq, a popular tool for SNP analysis, GenHtr is able to predict potential multiple variants that pre-exist in the bacterial population as well as SNPs that occur in the highly duplicated gene families. It is expected that, with the proper experimental design, this analysis can improve our understanding of the molecular mechanism underlying the dynamics and the evolution of drug-resistant bacterial pathogens. PMID:20939910

2010-01-01

349

Cipactlichthys scutatus, gen. nov., sp. nov. a new Halecomorph (Neopterygii, Holostei) from the Lower Cretaceous Tlayua Formation of Mexico.  

PubMed

Based on specimens from the Lower Cretaceous Tlayua Formation of Mexico, we describe a new genus and species of Halecomorphi, Cipactlichthysscutatus gen. et sp. nov, which exhibits several diagnostic characters such as the dermal bones and the scales with ganoin and highly ornamented by numerous tubercles and ridges; parietal slightly longer than wide with approximately the same length as the frontal; jaws extending far, below the posterior orbital margin, reaching the posterior third of the postorbital plate; maxilla with a convexly rounded posterior margin; pectoral fin margins slightly convex; first ray of pectoral fin very long, reaching the posterior edge of the pelvic fin; about 37 preural vertebrae and 7 Ural centra; a series of hypertrophied scales just posterior to the cleithrum; arrangement of flank scales with two rows of deep scales; a series of dorsal and ventral scutes forming the dorsal and ventral midline, between the dorsal and anal fins and the caudal fin. A phylogenetic analysis including two outgroups and eleven neopterygians confirmed the monophyly of the Holostei as well as the monophyly of the Halecomorphi, although this last clade is weakly supported. Cipactlichthysscutatus was hypothesised as the sister-group of the (Ionoscopiformes + Amiiformes). PMID:24023885

Brito, Paulo M; Alvarado-Ortega, Jesus

2013-01-01

350

The effects of angiotensinogen gene polymorphisms on cardiovascular disease outcomes during antihypertensive treatment in the GenHAT study  

PubMed Central

Previous studies have reported that risk of cardiovascular morbidity and mortality substantially increases in hypertensive patients, especially among those with inadequate blood pressure control. Two common antihypertensive drug classes including thiazide diuretics and angiotensin-converting enzyme (ACE) inhibitors affect different enzymes in the renin-angiotensin-aldosterone system (RAAS). In the RAAS, angiotensinogen is converted into angiotensin II which increases blood pressure through vasoconstriction. Using a case-only design with 3448 high-risk hypertensive individuals from the Genetics of Hypertension Associated Treatment (GenHAT) study, we examined whether seven single nucleotide polymorphisms (SNPs) in the angiotensinogen gene (AGT) interact with three classes of antihypertensive drugs including chlorthalidone (a thiazide diuretic), lisinopril (an ACE inhibitor), and amlodipine (a calcium channel blocker) to modify the risk of incident coronary heart disease (CHD) and heart failure (HF) among Caucasian and African American participants, separately. We found no gene by treatment interactions to be statistically significant after correction for multiple testing. However, some suggestive results were found. African American participants with the minor allele of rs11122576 had over two-fold higher risk of CHD when using chlorthalidone compared to using amlodipine, or lisinopril compared to amlodipine (p = 0.006 and p = 0.01, respectively). Other marginal associations are also reported among both race groups. The findings reported here suggest that rs11122576 could contribute to future personalization of antihypertensive treatment among African Americans though more studies are needed.

Do, Anh N.; Irvin, Marguerite R.; Lynch, Amy I.; Claas, Steven A.; Boerwinkle, Eric; Davis, Barry R.; Ford, Charles E.; Eckfeldt, John H.; Tiwari, Hemant K.; Limdi, Nita A.; Arnett, Donna K.

2014-01-01

351

The Ultramicrobacterium "Elusimicrobium minutum" gen. nov., sp. nov., the First Cultivated Representative of the Termite Group 1 Phylum? †  

PubMed Central

Insect intestinal tracts harbor several novel, deep-rooting clades of as-yet-uncultivated bacteria whose biology is typically completely unknown. Here, we report the isolation of the first representative of the termite group 1 (TG1) phylum from sterile-filtered gut homogenates of a humivorous scarab beetle larva. Strain Pei191T is a mesophilic, obligately anaerobic ultramicrobacterium with a gram-negative cell envelope. Cells are typically rod shaped, but cultures are pleomorphic in all growth phases (0.3 to 2.5 ?m long and 0.17 to 0.3 ?m wide). The isolate grows heterotrophically on sugars and ferments d-galactose, d-glucose, d-fructose, d-glucosamine, and N-acetyl-d-glucosamine to acetate, ethanol, hydrogen, and alanine as major products but only if amino acids are present in the medium. PCR-based screening and comparative 16S rRNA gene sequence analysis revealed that strain Pei191T belongs to the “intestinal cluster,” a lineage of hitherto uncultivated bacteria present in arthropod and mammalian gut systems. It is only distantly related to the previously described so-called “endomicrobia” lineage, which comprises mainly uncultivated endosymbionts of termite gut flagellates. We propose the name “Elusimicrobium minutum” gen. nov., sp. nov. (type strain, Pei191T = ATCC BAA-1559T = JCM 14958T) for the first isolate of this deep-branching lineage and the name “Elusimicrobia” phyl. nov. for the former TG1 phylum. PMID:19270135

Geissinger, Oliver; Herlemann, Daniel P. R.; Morschel, Erhard; Maier, Uwe G.; Brune, Andreas

2009-01-01

352

Isolation and characterization of Keratinibaculum paraultunense gen. nov., sp. nov., a novel thermophilic, anaerobic bacterium with keratinolytic activity.  

PubMed

A novel thermophilic, anaerobic, keratinolytic bacterium designated KD-1 was isolated from grassy marshland. Strain KD-1 was a spore-forming rod with a Gram-positive type cell wall, but stained Gram-negative. The temperature, pH, and NaCl concentration range necessary for growth was 30-65 °C (optimum 55 °C), 6.0-10.5 (optimum 8.0-8.5), and 0-6% (optimum 0.2%) (w/v), respectively. Strain KD-1 possessed extracellular keratinase, and the optimum activity of the crude enzyme was pH 8.5 and 70 °C. The enzyme was identified as a thermostable serine-type protease. The strain was sensitive to rifampin, chloramphenicol, kanamycin, and tetracycline and was resistant to erythromycin, neomycin, penicillin, and streptomycin. The main cellular fatty acid was predominantly C15:0 iso (64%), and the G+C content was 28 mol%. Morphological and physiological characterization, together with phylogenetic analysis based on 16S rRNA gene sequencing identified KD-1 as a new species of a novel genus of Clostridiaceae with 95.3%, 93.8% 16S rRNA gene sequence similarity to Clostridium ultunense BS(T) (DSM 10521(T)) and Tepidimicrobium xylanilyticum PML14(T) (= JCM 15035(T)), respectively. We propose the name Keratinibaculum paraultunense gen. nov., sp. nov., with KD-1 (=JCM 18769(T) =DSM 26752(T)) as the type strain. PMID:23710623

Huang, Yan; Sun, Yingjie; Ma, Shichun; Chen, Lu; Zhang, Hui; Deng, Yu

2013-08-01

353

Silanimonas lenta gen. nov., sp. nov., a slightly thermophilic and alkaliphilic gammaproteobacterium isolated from a hot spring.  

PubMed

A moderately thermophilic aerobic bacterium, strain 25-4T, was isolated from a hot spring at Baekdoo Mountain in Korea. The cells were Gram-negative, motile rods each having a polar flagellum. Analysis of the 16S rRNA gene sequence indicated that the strain represented a new lineage within the family 'Xanthomonadaceae' of the 'Gammaproteobacteria', being most closely related to the genera Thermomonas, Xanthomonas, Luteimonas, Pseudoxanthomonas, Stenotrophomonas and Xylella and having 16S rRNA gene sequence similarities to the most related species of the genera of between 92.9 and 94.4 %. The strain contained Q-8 as the major isoprenoid quinone and had a fatty acid profile with predominant iso-branched fatty acids. Growth occurred at pH 6.0-10, with an optimum at pH 9.0, and at 25-53 degrees C, with an optimum at 47 degrees C. The G+C content of the genomic DNA was 50.7 mol%. On the basis of phylogenetic analyses and its phenotypic characteristics, strain 25-4T belongs to a new genus, Silanimonas gen. nov., within the 'Gammaproteobacteria'. The sole species of this genus is Silanimonas lenta sp. nov. (type strain, 25-4T=DSM 16282T=KCTC 12236T). PMID:15653905

Lee, Eun Mi; Jeon, Che Ok; Choi, Inpyo; Chang, Kyu-Seob; Kim, Chang-Jin

2005-01-01

354

Permianibacter aggregans gen. nov., sp. nov., a bacterium of the family Pseudomonadaceae capable of aggregating potential biofuel-producing microalgae.  

PubMed

A novel bacterial strain, capable of aggregating potential biofuel-producing microalgae, was isolated from the phycosphere of an algal culture and designated HW001(T). The novel bacterial strain was identified on the basis of its phylogenetic, genotypic, chemotaxonomic and phenotypic characteristics in this study. Cells were aerobic, Gram-negative rods. 16S rRNA gene-based phylogenetic analysis revealed that strain HW001(T) is affiliated with the family Pseudomonadaceae in the phylum Proteobacteria, but forms a distinct clade within this family. The DNA G+C content of strain HW001(T) was 55.4 mol%. The predominant cellular fatty acids were iso-C15?:?0, summed feature 9 (iso-C17?:?1?9c), C16?:?0 and summed feature 3 (C16?:?1?7c/C16?:?1?6c). Q-8 was the main respiratory quinone. The polar lipid profile contained phosphatidylethanolamine, an unidentified aminophospholipid and some unidentified lipids. Based on the extensive polyphasic analysis, strain HW001(T) represents a novel species of a new genus in the family Pseudomonadaceae, for which the name Permianibacter aggregans gen. nov., sp. nov., is proposed. The type strain of the type species is HW001(T) (?=?CICC 10856(T)?=?KCTC 32485(T)). PMID:25052397

Wang, Hui; Zheng, Tianling; Hill, Russell T; Hu, Xiaoke

2014-10-01

355

Desulfohalophilus alkaliarsenatis gen. nov., sp. nov., an extremely halophilic sulfate- and arsenate-respiring bacterium from Searles Lake, California  

USGS Publications Warehouse

A haloalkaliphilic sulfate-respiring bacterium, strain SLSR-1, was isolated from a lactate-fed stable enrichment culture originally obtained from the extreme environment of Searles Lake, California. The isolate proved capable of growth via sulfate-reduction over a broad range of salinities (125–330 g/L), although growth was slowest at salt-saturation. Strain SLSR-1 was also capable of growth via dissimilatory arsenate-reduction and displayed an even broader range of salinity tolerance (50–330 g/L) when grown under these conditions. Strain SLSR-1 could also grow via dissimilatory nitrate reduction to ammonia. Growth experiments in the presence of high borate concentrations indicated a greater sensitivity of sulfate-reduction than arsenate-respiration to this naturally abundant anion in Searles Lake. Strain SLSR-1 contained genes involved in both sulfate-reduction (dsrAB) and arsenate respiration (arrA). Amplicons of 16S rRNA gene sequences obtained from DNA extracted from Searles Lake sediment revealed the presence of close relatives of strain SLSR-1 as part of the flora of this ecosystem despite the fact that sulfate-reduction activity could not be detected in situ. We conclude that strain SLSR-1 can only achieve growth via arsenate-reduction under the current chemical conditions prevalent at Searles Lake. Strain SLSR-1 is a deltaproteobacterium in the family Desulfohalobiacea of anaerobic, haloalkaliphilic bacteria, for which we propose the name Desulfohalophilus alkaliarsenatis gen. nov., sp. nov.

Blum, Jodi Switzer; Kulp, Thomas R.; Han, Sukkyun; Lanoil, Brian; Saltikov, Chad W.; Stolz, John F.; Miller, Laurence G.; Oremland, Ronald S.

2012-01-01

356

Ultrastructure and LSU rDNA-based phylogeny of Peridinium lomnickii and description of Chimonodinium gen. nov. (Dinophyceae).  

PubMed

Several populations of Peridinium lomnickii were examined by SEM and serial section TEM. Comparison with typical Peridinium, Peridiniopsis, Palatinus and Scrippsiella species revealed significant structural differences, congruent with phylogenetic hypotheses derived from partial LSU rDNA sequences. Chimonodinium gen. nov. is described as a new genus of peridinioids, characterized by the Kofoidian plate formula Po, cp, x, 4', 3a, 7'', 6c, 5s, 5''', 2'''', the absence of pyrenoids, the presence of a microtubular basket with four or five overlapping rows of microtubules associated with a small peduncle, a pusular system with well-defined pusular tubes connected to the flagellar canals, and the production of non-calcareous cysts. Serial section examination of Scrippsiella trochoidea, here taken to represent typical Scrippsiella characters, revealed no peduncle and no associated microtubular strands. The molecular phylogeny placed C. lomnickii comb. nov. as a sister group to a clade composed of Thoracosphaera and the pfiesteriaceans. Whereas the lack of information on fine structure of the swimming stage of Thoracosphaera leaves its affinities unexplained, C. lomnickii shares with the pfiesteriaceans the presence of a microtubular basket and the unusual connection between two plates on the left side of the sulcus, involving extra-cytoplasmic fibres. PMID:21621455

Craveiro, Sandra C; Calado, António J; Daugbjerg, Niels; Hansen, Gert; Moestrup, Øjvind

2011-10-01

357

Alkaliphilus transvaalensis gen. nov., sp. nov., an extremely alkaliphilic bacterium isolated from a deep South African gold mine  

SciTech Connect

A novel extreme alkaliphile was isolated from a mine water containment dam at 3.2 km bellow land surface in an ultra-deep gold mine near Carletonville, South Africa. The cells of this bacterium were straight to slightly curved rods, motile by flagella and formed endospores, Growth was observed over the temperature range 20-50 degreesC (optimum 40 degreesC; 45 min doubling time) and ph range 8.5-12.5 (optimum pH 10.0). The novel isolate, one of the most alkaliphilic micro-organisms yet described, was a strictly anaerobic chemo-organotroph capable of utilizing proteinaceous substrates such as yeast extract, peptone. tryptone and casein, Elemental sulfur, thiosulfate or fumarate, when included as accessory electron acceptors, improved growth. The G+C content of genomic DNA was 36.4 mol%, Phylogenetic analysis based on the 16S rDNA sequence indicated that the isolate is a member of cluster XI within the low G+C Cram-positive bacteria, but only distantly related to previously described members. On the basis of physiological and molecular properties, the isolate represents a novel species, for which the name Alkaliphilus transvaalensis gen. nov., sp. nov. is proposed (type strain SAGM1(T)= JCM 10712(T)= ATCC 700919(T)). The mechanism of generation of the highly alkaline microbial habitat and the possible source of the alkaliphile are discussed.

Takai, Ken; Moser, Duane P.; Onstott, Tullis C.; Spoelstra, N; Pfiffner, Susan M.; Dohnalkova, Alice; Fredrickson, Jim K.

2001-07-01

358

Cipactlichthys scutatus, gen. nov., sp. nov. a New Halecomorph (Neopterygii, Holostei) from the Lower Cretaceous Tlayua Formation of Mexico  

PubMed Central

Based on specimens from the Lower Cretaceous Tlayua Formation of Mexico, we describe a new genus and species of Halecomorphi, Cipactlichthysscutatus gen. et sp. nov, which exhibits several diagnostic characters such as the dermal bones and the scales with ganoin and highly ornamented by numerous tubercles and ridges; parietal slightly longer than wide with approximately the same length as the frontal; jaws extending far, below the posterior orbital margin, reaching the posterior third of the postorbital plate; maxilla with a convexly rounded posterior margin; pectoral fin margins slightly convex; first ray of pectoral fin very long, reaching the posterior edge of the pelvic fin; about 37 preural vertebrae and 7 Ural centra; a series of hypertrophied scales just posterior to the cleithrum; arrangement of flank scales with two rows of deep scales; a series of dorsal and ventral scutes forming the dorsal and ventral midline, between the dorsal and anal fins and the caudal fin. A phylogenetic analysis including two outgroups and eleven neopterygians confirmed the monophyly of the Holostei as well as the monophyly of the Halecomorphi, although this last clade is weakly supported. Cipactlichthysscutatus was hypothesised as the sister-group of the (Ionoscopiformes + Amiiformes). PMID:24023885

Brito, Paulo M.; Alvarado-Ortega, Jesus

2013-01-01

359

Haloalkaliphilic spore-forming sulfidogens from soda lake sediments and description of Desulfitispora alkaliphila gen. nov., sp. nov.  

PubMed Central

An anaerobic enrichment with pyruvate as electron donor and thiosulfate at pH 10 and 0.6 M Na+ inoculated with pasteurized soda lake sediments resulted in a sulfidogenic coculture of two morphotypes of obligately anaerobic haloalkaliphilic endospore-forming clostridia, which were further isolated in pure culture. Strain AHT16 was a thin long rod able to ferment sugars and pyruvate and to respire H2, formate and pyruvate using thiosulfate and fumarate as electron acceptors and growing optimally at pH 9.5. Thiosulfate was reduced incompletely to sulfide and sulfite. The strain was closely related (99% sequence similarity) to a peptolytic alkaliphilic clostridium Natronincola peptidovorans. Strain AHT17 was a short rod with a restricted respiratory metabolism, growing with pyruvate and lactate as electron donor and sulfite, thiosulfate and elemental sulfur as electron acceptors with a pH optimum 9.5. Thiosulfate was reduced completely via sulfite to sulfide. The ability of AHT17 to use sulfite explained the stability of the original coculture of the two clostridia—one member forming sulfite from thiosulfate and another consuming it. Strain AHT17 formed an independent deep phylogenetic lineage within the Clostridiales and is proposed as a new genus and species Desulfitisporum alkaliphilum gen. nov., sp. nov. (=DSM 22410T = UNIQEM U794T). Electronic supplementary material The online version of this article (doi:10.1007/s00792-010-0310-y) contains supplementary material, which is available to authorized users. PMID:20364356

Muyzer, Gerard

2010-01-01

360

Morphology and ontogenesis of Psilotrichides hawaiiensis nov. gen., nov. spec. and molecular phylogeny of the Psilotrichidae (Ciliophora, Hypotrichia).  

PubMed

The Psilotrichidae are a family of middle-sized hypotrichs with unique morphological and ontogenetic features (e.g. the oral primordium develops in a deep pouch) that, however, did not provide a definite phylogenetic signal. Thus, we studied the 18S rRNA gene of Urospinula succisa (Müller 1786) Esteban et al., 2001 as well as the morphology and ontogenesis of Psilotrichides hawaiiensis, a new genus and species from an ephemeral swamp on Oahu Island, Hawaii. The molecular data classify the psilotrichids into the oxytrichids but without clear branching position. A brief revision, using the structure of the oral apparatus, the location of the contractile vacuole, and three ontogenetic features, showed four distinct genera: Psilotricha Stein, 1859; Urospinula Corliss, 1960; Hemiholosticha Gelei, 1954; and Psilotrichides nov. gen., which differs from the confamilials mainly by the obliquely oriented buccal cavity and the shape of the undulating membranes as well as by a distinct ridge along the right buccal margin. The pyriform species, P. hawaiiensis, is about 65 × 45 ?m in size and is easily recognized by the table tennis racket-shaped appearance due to the elongated last cirrus of the left marginal row. Refined diagnoses are provided for the family Psilotrichidae Bütschli, 1889 and the genera contained. PMID:24498929

Heber, Domingo; Stoeck, Thorsten; Foissner, Wilhelm

2014-01-01

361

Pelagibaca bermudensis gen. nov., sp. nov., a novel marine bacterium within the Roseobacter clade in the order Rhodobacterales.  

PubMed

A Gram-negative, chemoheterotrophic, facultatively anaerobic, slightly halophilic, oval-shaped marine bacterium, designated HTCC2601T, was isolated from the western Sargasso Sea by high-throughput culturing involving dilution to extinction. Although the 16S rRNA gene sequence similarity between the isolate and Salipiger mucosus was 96.5 %, phylogenetic analyses using different treeing algorithms clearly indicated that the strain forms a distinct lineage within a clade containing the recently classified genera Salipiger and Palleronia in the order Rhodobacterales of the Alphaproteobacteria. The DNA-DNA relatedness between strain HTCC2601T and S. mucosus was 26.3 %. Strain HTCC2601T utilized a wide range of carbohydrates, including hexose monomers, sugar alcohols, organic acids and amino acids, as sole carbon sources. The DNA G+C content of strain HTCC2601T was 65.4 mol%, and the predominant constituents of the cellular fatty acids were 18 : 1omega7c (79.7 %) and 11-methyl 18 : 1omega7c (7.5 %). The strain differed from members of the closely related genera Salipiger and Palleronia in its morphological, biochemical and ecological characteristics. On the basis of the taxonomic data obtained in this study, a novel genus and species, Pelagibaca bermudensis gen. nov., sp. nov., is proposed; HTCC2601T (=KCTC 12554T = JCM 13377T) is the type strain of Pelagibaca bermudensis. PMID:16585706

Cho, Jang-Cheon; Giovannoni, Stephen J

2006-04-01

362

Fastidiosipila sanguinis gen. nov., sp. nov., a new Gram-positive, coccus-shaped organism from human blood.  

PubMed

Phenotypic and phylogenetic studies were performed on two strains of an unidentified Gram-positive, fastidious, non-spore-forming, coccus-shaped bacterium recovered from human blood. The organism was catalase-negative and grew under strictly anaerobic conditions and in the presence of 2 and 6 % O(2). Comparative 16S rRNA gene sequencing demonstrated that the unidentified bacterium was, phylogenetically, far removed from peptostreptococci and related Gram-positive coccus-shaped organisms, but exhibited a phylogenetic association with Clostridium rRNA cluster III [as defined by Collins et al., Int J Syst Bacteriol 44 (1994), 812-826]. Sequence divergence values of 15 % or more were observed between the unidentified bacterium and all other recognized species within this and related rRNA clostridial clusters. Treeing analysis showed that the unknown bacterium formed a deep line branching at the periphery of rRNA cluster III and represents a hitherto unknown genus within this supra-generic grouping. On the basis of both phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from blood be classified in a new genus, Fastidiosipila gen. nov., as Fastidiosipila sanguinis sp. nov. The type strain of Fastidiosipila sanguinis is CCUG 47711(T) (=CIP 108292(T)). PMID:15774674

Falsen, Enevold; Collins, Matthew D; Welinder-Olsson, Christina; Song, Yuli; Finegold, Sydney M; Lawson, Paul A

2005-03-01

363

Methylibium petroleiphilum gen. nov., sp. nov., a novel methyl tert-butyl ether-degrading methylotroph of the Betaproteobacteria.  

PubMed

A Gram-negative, rod-shaped, motile, non-pigmented, facultative aerobe that grew optimally at pH 6.5 and 30 degrees C (strain PM1T) was isolated for its ability to completely degrade the gasoline additive methyl tert-butyl ether. Analysis of the 16S rRNA gene sequence indicated that this bacterium was a member of the class Betaproteobacteria in the Sphaerotilus-Leptothrix group. The 16S rRNA gene sequence identity to other genera in this group, Leptothrix, Aquabacterium, Roseateles, Sphaerotilus, Ideonella and Rubrivivax, ranged from 93 to 96 %. The chemotaxonomic data including Q-8 as the major quinone, C16 : 1omega7c and C16 : 0 as the major fatty acids and a DNA G+C content of 69 mol%, support the inclusion of strain PM1T in the class Betaproteobacteria. It differed from other members of the Sphaerotilus-Leptothrix group by being a facultative methylotroph that used methanol as a sole carbon source, and by also being able to grow heterotrophically in defined media containing ethanol, toluene, benzene, ethylbenzene and dihydroxybenzoates as sole carbon sources. On the basis of the morphological, physiological, biochemical and genetic information, a new genus and species, Methylibium petroleiphilum gen. nov., sp. nov., is proposed, with PM1T (=ATCC BAA-1232T=LMG 22953T) as the type strain. PMID:16627642

Nakatsu, Cindy H; Hristova, Krassimira; Hanada, Satoshi; Meng, Xian-Ying; Hanson, Jessica R; Scow, Kate M; Kamagata, Yoichi

2006-05-01

364

Bavariicoccus seileri gen. nov., sp. nov., isolated from the surface and smear water of German red smear soft cheese.  

PubMed

The phylogenetic position and physiological characters of six hitherto-unknown lactic acid bacterial isolates, which form part of the surface microbiota of German red smear soft cheese, are reported. The coccoid cells are aerotolerant, Gram-positive, catalase-negative and non-motile. The cell-wall peptidoglycan contains alanine, glutamic acid, lysine and aspartic acid and is of the A4alpha type (l-Lys-d-Asp). The sequences of the 16S rRNA, groEL and rpoB genes of the six isolates are identical and reveal that these isolates represent an independent lineage within the radiation of the family Enterococcaceae in the phylum Firmicutes. Their closest phylogenetic neighbour is the lactic acid bacterium Atopobacter phocae M1590/94/2(T), with which they share 94.9 % 16S rRNA gene sequence similarity; representatives of other genera such as Granulicatella, Carnobacterium and Trichococcus are more distantly related. DNA-DNA hybridization studies reveal that the six isolates are members of a single species, and this is confirmed by similarities in biochemical characteristics. The six isolates were assigned four different groups by Fourier-transform infrared and randomly amplified polymorphic DNA typing. Therefore, it is formally proposed that these isolates should be classified in a single novel species of a novel genus and be named Bavariicoccus seileri gen. nov., sp. nov. The type strain of Bavariicoccus seileri is WCC 4188(T) (=DSM 19936(T) =CCUG 55508(T)). PMID:19622668

Schmidt, Verena S J; Mayr, Ralf; Wenning, Mareike; Glöckner, Jana; Busse, Hans-Jürgen; Scherer, Siegfried

2009-10-01

365

Streptohalobacillus salinus gen. nov., sp. nov., a moderately halophilic, Gram-positive, facultative anaerobe isolated from subsurface saline soil.  

PubMed

A Gram-stain-positive, rod-shaped, non-sporulating, motile and moderately halophilic bacterium, designated strain H96B60(T), was isolated from a saline soil sample of the Qaidam basin, China. The strain was facultatively anaerobic. Major end products formed from glucose fermentation were acetate, ethanol and lactic acid. The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The isoprenoid quinone component was menaquinone-6 (MK-6). The predominant cellular fatty acids were C(16: 0), anteiso-C(13 : 0) and anteiso-C(15 : 0). The genomic DNA G+C content of strain H96B60(T) was 36.2 mol%. Phylogenetic analysis based on comparative 16S rRNA gene sequences indicated that strain H96B60(T) represented a novel phyletic lineage within the family Bacillaceae and was related most closely to Halolactibacillus species (96.1-96.4 % similarity). Based on the phenotypic, chemotaxonomic and phylogenetic data presented, strain H96B60(T) is considered to represent a novel species of a new genus, for which the name Streptohalobacillus salinus gen. nov., sp. nov. is proposed. The type strain of Streptohalobacillus salinus is H96B60(T) (?=?DSM 22440(T) ?=?CGMCC 1.7733(T)). PMID:20543154

Wang, Xiaowei; Xue, Yanfen; Ma, Yanhe

2011-05-01

366

Ultrastructure and molecular phylogenetic position of Neometanema parovale sp. nov. (Neometanema gen. nov.), a Marine phagotrophic euglenid with skidding motility.  

PubMed

Heteronema is a commonly encountered genus of phagotrophic euglenids that contains very different morphotypes, including elongate gliding species and ovoid skidding forms. We report the first ultrastructural and sequence data from a culture of an ovoid skidding heteronemid, KM051. Cells were 8-23.5 ?m long with 22 pellicular strips and a fibrous extracellular layer. The tubular extrusomes had dense centre sections. The feeding apparatus was barely visible by light microscopy, but included two microtubule-supported rods. The flagella had hollow, inflated transition zones, heteromorphic paraxonemal rods, and sheaths of flagellar hairs. The posterior flagellum bore a knob that, unusually, sat >2 ?m distal to the flagellar base. No ultrastructural features were uniquely shared by KM051 and the elongate, gliding species Heteronema scaphurum. Conversely, the pellicular microtubule array resembles that in deep-branching primary osmotrophs (Aphagea). 18S ribosomal DNA (18S rDNA) phylogenies showed that KM051 is related to a recently obtained Heteronema c.f. exaratum sequence. These skidding heteronemids are not closely related to H. scaphurum, and instead are closely related to Dinema, Anisonema and specifically, Aphagea. The skidding species in Heteronema are transferred to Neometanema gen. nov. (along with most species of Metanema Klebs, 1893), with KM051 described as Neometanema parovale sp. nov. PMID:24945929

Lee, Won Je; Simpson, Alastair G B

2014-08-01

367

Desulfatiferula olefinivorans gen. nov., sp. nov., a long-chain n-alkene-degrading, sulfate-reducing bacterium.  

PubMed

A novel anaerobic, long-chain alkene-degrading, sulfate-reducing bacterium, strain LM2801T, was isolated from brackish sediment of a wastewater decantation facility of an oil refinery (Berre lagoon, France). Cells of strain LM2801T were Gram-negative, motile, slightly curved or vibrioid rods. Its optimum growth conditions were 30-36 degrees C, 6-10 g NaCl l(-1) and pH 7.5. Strain LM2801T incompletely oxidized long-chain alkenes (from C14 to C23) and fatty acids (C14 to C24). The DNA G+C content was 45.5 mol%. Sequence analyses of the 16S rRNA and dsrAB genes indicated that the strain was a member of the family Desulfobacteraceae within the Deltaproteobacteria. This novel isolate possesses phenotypic and phylogenetic traits that do not allow its classification as a member of any previously described genus. Therefore, strain LM2801T is described as a member of a new genus, Desulfatiferula gen. nov., of which Desulfatiferula olefinivorans sp. nov. is the type species. The type strain of Desulfatiferula olefinivorans is LM2801T (=DSM 18843T=JCM 14469T). PMID:17978243

Cravo-Laureau, Cristiana; Labat, Cindy; Joulian, Catherine; Matheron, Robert; Hirschler-Réa, Agnès

2007-11-01

368

Desulfatibacillum aliphaticivorans gen. nov., sp. nov., an n-alkane- and n-alkene-degrading, sulfate-reducing bacterium.  

PubMed

A novel marine sulfate-reducing bacterium, strain CV2803T, which is able to oxidize aliphatic hydrocarbons, was isolated from a hydrocarbon-polluted marine sediment (Gulf of Fos, France). The cells were rod-shaped and slightly curved, measuring 0.6x2.2-5.5 microm. Strain CV2803T stained Gram-negative and was non-motile and non-spore-forming. Optimum growth occurred in the presence of 24 g NaCl l(-1), at pH 7.5 and at a temperature between 28 and 35 degrees C. Strain CV2803T oxidized alkanes (from C13 to C18) and alkenes (from C7 to C23). The DNA G+C content was 41.4 mol%. Comparative sequence analyses of the 16S rRNA gene and dissimilatory sulfite reductase (dsrAB) gene and those of other sulfate-reducing bacteria, together with its phenotypic properties, indicated that strain CV2803T was a member of a distinct cluster that contained unnamed species. Therefore, strain CV2803T (=DSM 15576T=ATCC BAA-743T) is proposed as the type strain of a novel species in a new genus, Desulfatibacillum aliphaticivorans gen. nov., sp. nov. PMID:14742462

Cravo-Laureau, Cristiana; Matheron, Robert; Cayol, Jean-Luc; Joulian, Catherine; Hirschler-Réa, Agnès

2004-01-01

369

Bacterioplanes sanyensis gen. nov., sp. nov., a PHB-accumulating bacterium isolated from a pool of Spirulina platensis cultivation.  

PubMed

A Gram-negative, poly-3-hydroxybutyrate-accumulating rod bacterium, strain GYP-2(T), was isolated from a pool of marine Spirulina platensis cultivation, Sanya, China. Growth was observed at 10-45 °C and pH 6-10 in the presence of 1-10 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the new isolate belonged to Gammaproteobacteria and displayed 93.8-95.3 % 16S rRNA gene sequences similarities to members of the genera Thalassolituus, Oleibacter, and Oceanobacter, but house-keeping gene gyrB (encode DNA gyrase beta subunit) demonstrated that the new isolate was distantly related to Thalassolituus, Oleibacter, and Oceanobacter species (only 77-83 % gene gyrB sequences similarities).The G+C content of genomic DNA was 55 mol%. The major respiratory quinone was Q-9, while that for Oceanobacter kriegii LMG 6238(T) was Q-8. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. On the basis of its physiological, chemotaxonomic, and molecular properties, strain GYP-2(T) is suggested to represent a novel species of a new genus in Gammaproteobacteria, for which the name Bacterioplanes sanyensis gen. nov., sp. nov. is proposed. The type strain is GYP-2(T) (=CGMCC 1.12392(T)=KCTC 32220(T)). PMID:25038945

Wang, Guanghua; Jia, Qikun; Li, Tao; Dai, Shikun; Wu, Huanlian; He, Hui; Fan, Jiewei; Xiang, Wenzhou; Li, Xiang

2014-10-01

370

Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney.  

PubMed

A novel barophilic, hyperthermophilic archaeon was isolated from a deep-sea hydrothermal vent chimney at the Myojin Knoll in the Ogasawara-Bonin Arc, Japan. The cells were found to be irregular cocci and motile with multiple polar flagella. Growth was observed between 60 and 88 degrees C (opt. 83 degrees C; 30 min doubling time), pH 4.0 and 8.0 (opt. pH 6.0), 20 and 73 g sea salts l-1 (opt. 47 g l-1) and 0.1 and 60 MPa (opt. 30 MPa). The isolate was a strictly anaerobic chemoorganotroph capable of utilizing proteinaceous substrates such as yeast extract, peptone, tryptone and casein in the presence of elemental sulfur or ferrous iron. The G + C content of the genomic DNA was 53.5 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that the isolate was a member of an ancient lineage of the Thermococcales that diverged prior to the formation of the two genera Thermococcus and Pyrococcus. On the basis of the physiological and molecular properties of the new isolate, the name Palaeococcus ferrophilus gen. nov., sp. nov. is proposed. The type strain is strain DMJT (= JCM 10417) [corrected]. PMID:10758851

Takai, K; Sugai, A; Itoh, T; Horikoshi, K

2000-03-01

371

Moorea producens gen. nov., sp. nov. and Moorea bouillonii comb. nov., tropical marine cyanobacteria rich in bioactive secondary metabolites  

PubMed Central

The filamentous cyanobacterial genus Moorea gen. nov., described here under the provisions of the International Code of Botanical Nomenclature, is a cosmopolitan pan-tropical group abundant in the marine benthos. Members of the genus Moorea are photosynthetic (containing phycocyanin, phycoerythrin, allophycocyanin and chlorophyll a), but non-diazotrophic (lack heterocysts and nitrogenase reductase genes). The cells (discoid and 25–80 µm wide) are arranged in long filaments (<10 cm in length) and often form extensive mats or blooms in shallow water. The cells are surrounded by thick polysaccharide sheaths covered by a rich diversity of heterotrophic micro-organisms. A distinctive character of this genus is its extraordinarily rich production of bioactive secondary metabolites. This is matched by genomes rich in polyketide synthase and non-ribosomal peptide synthetase biosynthetic genes which are dedicated to secondary metabolism. The encoded natural products are sometimes responsible for harmful algae blooms and, due to morphological resemblance to the genus Lyngbya, this group has often been incorrectly cited in the literature. We here describe two species of the genus Moorea: Moorea producens sp. nov. (type species of the genus) with 3LT as the nomenclature type, and Moorea bouillonii comb. nov. with PNG5-198R as the nomenclature type. PMID:21724952

Engene, Niclas; Rottacker, Erin C.; Kastovsky, Jan; Byrum, Tara; Choi, Hyukjae; Ellisman, Mark H.; Komarek, Jiri

2012-01-01

372

Iapetonudus (N. gen.) and Iapetognathus Landing, unusual Earliest Ordovician multielement conodont taxa and their utility for biostratigraphy  

USGS Publications Warehouse

The Early Ordovician (Tremadocian) multielement conodont genus Iapetognathus is one of the oldest denticulate euconodont genera known. The ramiform-ramiform apparatus structure of Iapetognathus is not similar morphologically to other Late Cambrian to Earliest Ordovician denticulate multielement taxa, such as Eodentatus or Cordyloduts, because the major denticulate process has a lateral rather than a posterior orientation as it is in the other two examples. For this reason the genus is believed to have developed from the coniform-coniform apparatus Iapetonudus ibexensis (N.gen., n.sp.) through the development of the denticulate lateral processes. The two genera have a number of morphologic features in common and appear in stratigraphic succession. Iapetognathus aengensis (Lindstro??m) is redefined as a multielement taxon using topotype material and Ig. preaengensis Landing is placed in synonymy with it. Iapetognathus sprakersi, recently described by Landing in Landing and others (1996), is recognized as a multielement species and the new multielement species, Ig. fluctivagus, Ig. jilinensis and Ig. landingi n. spp. are described herein, based on type specimens from Utah (U.S.A.), Jilin (China) and Colorado (U.S.A.) respectively. Iapetonudus and Iapetognathus are important genera in defining the level of the Cambrian-Ordovician boundary. Iapetonudus is currently recognized only from Utah, Texas and Oklahoma, but Iapetognathus is cosmopolitan in its distribution.

Nicoll, R. S.; Miller, J. F.; Nowlan, G. S.; Repetski, J. E.; Ethington, R. L.

1999-01-01

373

Lacihabitans soyangensis gen. nov., sp. nov., a new member of the family Cytophagaceae, isolated from a freshwater reservoir.  

PubMed

A Gram-staining-negative, non-motile and orange-pigmented bacterium, designated strain HME6675(T), was isolated from freshwater of a reservoir in Korea. The major fatty acids of strain HME6675(T) were iso-C15?:?0 (33.4?%) and summed feature 3 (comprising C16?:?1?6c and/or C16?:?1?7c; 31.3?%). The major respiratory quinone was MK-7. The polar lipids were phosphatidylethanolamine, one unidentified aminolipid, one unidentified aminophospholipid and three unidentified polar lipids. The DNA G+C content of strain HME6675(T) was 37.7 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HME6675(T) formed a lineage within the family Cytophagaceae and was related to Leadbetterella byssophila 4M15(T) (93.0?% sequence similarity), Fluviimonas pallidilutea TQQ6(T) (90.6?%) and Emticicia oligotrophica GPTSA100-15(T) (89.1?%). On the basis of the evidence presented in this study, strain HME6675(T) represents a novel genus and species of the family Cytophagaceae, for which the name Lacihabitans soyangensis gen. nov., sp. nov. is proposed. The type strain of Lacihabitans soyangensis is HME6675(T) (?=?KCTC 23259(T)?=?CECT 7826(T)). PMID:24994775

Joung, Yochan; Kim, Haneul; Kang, Heeyoung; Lee, Beom-Il; Ahn, Tae-Seok; Joh, Kiseong

2014-09-01

374

Minicystis rosea gen. nov., sp. nov., a polyunsaturated fatty acid-rich and steroid-producing soil myxobacterium.  

PubMed

A bacterial strain designated SBNa008(T) was isolated from a Philippine soil sample. It exhibited the general characteristics associated with myxobacteria, such as swarming of Gram-negative vegetative rod cells, fruiting body and myxospore formation and predatory behaviour in lysing micro-organisms. The novel strain was characterized as mesophilic, chemoheterotrophic and aerobic. The major fatty acids were C20?:?4?6,9,12,15 all cis (arachidonic acid), iso-C15?:?0, C17?:?1 2-OH and iso-C15?:?0 dimethylacetal. Interestingly, SBNa008(T) contained diverse fatty acids belonging to the commercially valuable polyunsaturated omega-6 and omega-3 families, and a highly conjugated dihydroxylated C28 steroid. The G+C content of the genomic DNA was 67.3 mol%. The 16S rRNA gene sequence revealed 95-96?% similarity to sequences derived from clones of uncultured bacteria and 94-95?% similarity to cultured members of the suborder Sorangiineae. Phylogenetic analysis revealed that strain SBNa008(T) formed a novel lineage in the suborder Sorangiineae. Based on a polyphasic taxonomic characterization, we propose that strain SBNa008(T) represents a novel genus and species, Minicystis rosea gen. nov., sp. nov. The type strain of Minicystis rosea is SBNa008(T) (?=?DSM 24000(T)?=?NCCB 100349(T)). PMID:25114157

Garcia, Ronald; Gemperlein, Katja; Müller, Rolf

2014-11-01

375

Umboniibacter marinipuniceus gen. nov., sp. nov., a marine gammaproteobacterium isolated from the mollusc Umbonium costatum from the Sea of Japan.  

PubMed

Two bacterial strains, KMM 3891(T) and KMM 3892, were isolated from internal tissues of the marine mollusc Umbonium costatum collected from the Sea of Japan. The novel isolates were Gram-negative, aerobic, faint pink-reddish-pigmented, rod-shaped, non-motile, stenohaline and psychrotolerant bacteria that were unable to degrade most tested complex polysaccharides. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Fatty acid analysis revealed C(17 : 1)omega6c, C(17 : 0), C(16 : 0) and C(16 : 1)omega7c as the dominant components. The major isoprenoid quinone was Q-7. The DNA G+C content of strain KMM 3891(T) was 51.7 mol%. According to phylogenetic analysis of 16S rRNA gene sequences, strains KMM 3891(T) and KMM 3892 were positioned within the Gammaproteobacteria as a separate branch, sharing <93 % sequence similarity to their phylogenetic relatives including Saccharophagus degradans, Microbulbifer species, Endozoicomonas elysicola, Simiduia agarivorans and Teredinibacter turnerae. Based on phenotypic characterization and phylogenetic distance, the novel marine isolates KMM 3891(T) and KMM 3892 represent a new genus and species, for which the name Umboniibacter marinipuniceus gen. nov., sp. nov. is proposed. The type strain of Umboniibacter marinipuniceus is KMM 3891(T) (=NRIC 0753(T) =JCM 15738(T)). PMID:19654350

Romanenko, Lyudmila A; Tanaka, Naoto; Frolova, Galina M

2010-03-01

376

Photoionization studies of germanium and tin clusters in the energy region of 5.0-8.8 eV: Ionization potentials for Gen (n=2-57) and Snn (n=2-41)  

NASA Astrophysics Data System (ADS)

Photoionization thresholds for Gen (n?57) and Snn (n?41) are examined by laser photoionization with detection by reflectron time-of-flight mass spectrometry. Stimulated Raman anti-Stokes scattering of narrow bandwidth 193, 248, and 266 nm radiation is used to produce ionization light sources in the vacuum ultraviolet region (200-141 nm). A very similar size dependence of the ionization potentials (IPs) is found for germanium and tin clusters with fewer than 12 atoms, featuring a major maximum at n=10. The rather high IP of Ge10 compared with its neighbors is consistent with the results of a photodissociation study of Gen+. We also find a rapid decrease in the IPs for Gen between n=15 and 26, which is very similar to that for silicon clusters reported in our previous paper. On the other hand, the IPs of medium size Snn (n=15-41) clusters are found to decrease slowly without such a gap. The remarkable difference in the size dependence of the IPs for the Sin, Gen, and Snn clusters is discussed in relation to the existence of a structural transition in the medium-size Sin and Gen clusters.

Yoshida, Shinji; Fuke, Kiyokazu

1999-09-01

377

"GEnAge": GenAge  

E-print Network

. Cereviseae C.elegans Mus musculus Human cells Genome surveillance, Proteasome Mitochondrial metabolism for application: 23 December 2013 Macromolecular damage Aging Longevity S. Cereviseae C.elegans Mus musculus

378

Genetic relationships among avian isolates classified as Pasteurella haemolytica, 'Actinobacillus salpingitidis' or Pasteurella anatis with proposal of Gallibacterium anatis gen. nov., comb. nov. and description of additional genomospecies within Gallibacterium gen. nov.  

PubMed

Bacteria of the avian [Pasteurella haemolytica]-'Actinobacillus salpingitidis' complex have been associated with different pathological conditions in birds, among which salpingitis and peritonitis in chickens of layer type seem to dominate. The aim of this study was to classify these bacteria by comparison of 37 strains tentatively classified as biovars of the avian [P. haemolytica]-'A. salpingitidis' complex or as Pasteurella anatis. PFGE, AFLP and plasmid profiling showed that strains representing different biovars were genotypically different. Phylogenetic analysis of 22 strains characterized by 16S rRNA gene sequence comparison showed that strains classified as biovars 5, 8 and 9 were closely related to the suggested type strain of 'A. salpingitidis' (98.4-99.9% similarity), whereas the remaining strains classified in 12 biovars or as P. anatis were closely related to the type strain of P. anatis (98.1-100% similarity). The two groups were related at 95.7-97.1% similarity. The closest similarity outside this group was 94.6%, between biovar 15 and Bisgaard taxon 3. DNA-DNA hybridization was performed with 34 strains and showed binding above 85% for strains of biovars 5 and 8, including the suggested type strain of 'A. salpingitidis'. Two strains of P. anatis (F 149T and F 279) were closely related at 79% DNA binding to 27 strains of biovars 1,3, 4, 11, 12, 17-20, 22 and 24. A new genus, Gallibacterium gen. nov., is proposed to include the avian [P. haemolytica]-'A. salpingitidis'-P. anatis complex, since these taxa form a monophyletic unit with similarities above 95% on the basis of 16S rRNA sequence comparison and they are unrelated to other genera of the family Pasteurellaceae Pohl 1981. The new genus consists of Gram-negative, non-motile, rod-shaped or pleomorphic bacteria. The bacteria are catalase-, oxidase- and phosphatase-positive. Nitrate is reduced and acid is produced without gas formation from glycerol, (-)D-ribose, (+)D-xylose, (-)D-mannitol, (-)D-fructose, (+)D-galactose, (+)D-glucose, (+)D-mannose, sucrose and raffinose. The genus Gallibacterium can be separated from other genera of Pasteurellaceae by differences in catalass, symbiotic growth, haemolysis, urease, indole, acid production from (+)D-xylose, (-)D-mannitol, (-)D-sorbitol, (+)D-mannose, maltose, raffinose and dextrin and ONPG and PNPG tests. Pasteurella anatis Mutters et al. 1985 is transferred to the new genus as Gallibacterium anatis gen. nov., comb. nov. Genomospecies 1 of Gallibacterium is proposed to include the former biovars 5 and 8 of the avian [P. haemolytica]-'A. salpingitidis' complex. The type strain of Gallibacterium anatis is F 149T (=ATCC 43329T = NCTC 11413T) and the reference strain of Gallibacterium genomospecies 1 is CCM 5974. PMID:12656185

Christensen, Henrik; Bisgaard, Magne; Bojesen, Anders Miki; Mutters, Reinier; Olsen, John Elmerdahl

2003-01-01

379

The role of SNP-loop diuretic interactions in hypertension across ethnic groups in HyperGEN  

PubMed Central

Blood pressure (BP) is significantly influenced by genetic factors; however, less than 3% of the BP variance has been accounted for by variants identified from genome-wide association studies (GWAS) of primarily European-descent cohorts. Other genetic influences, including gene-environment (GxE) interactions, may explain more of the unexplained variance in BP. African Americans (AA) have a higher prevalence and earlier age of onset of hypertension (HTN) as compared with European Americans (EA); responses to anti-hypertensive drugs vary across race groups. To examine potential interactions between the use of loop diuretics and HTN traits, we analyzed systolic (SBP) and diastolic (DBP) blood BP from 1222 AA and 1231 EA participants in the Hypertension Genetic Epidemiology Network (HyperGEN). Population-specific score tests were used to test associations of SBP and DBP, using a panel of genotyped and imputed single nucleotide polymorphisms (SNPs) for AA (2.9 million SNPs) and EA (2.3 million SNPs). Several promising loci were identified through gene-loop diuretic interactions, although no SNP reached genome-wide significance after adjustment for genomic inflation. In AA, SNPs in or near the genes NUDT12, CHL1, GRIA1, CACNB2, and PYHIN1 were identified for SBP, and SNPs near ID3 were identified for DBP. For EA, promising SNPs for SBP were identified in ESR1 and for DBP in SPATS2L and EYA2. Among these SNPs, none were common across phenotypes or population groups. Biologic plausibility exists for many of the identified genes, suggesting that these are candidate genes for regulation of BP and/or anti-hypertensive drug response. The lack of genome-wide significance is understandable in this small study employing gene-drug interactions. These findings provide a set of prioritized SNPs/candidate genes for future studies in HTN. Studies in more diversified population samples may help identify previously missed variants. PMID:24400021

de Las Fuentes, Lisa; Sung, Yun Ju; Schwander, Karen L.; Kalathiveetil, Sonia; Hunt, Steven C.; Arnett, Donna K.; Rao, D. C.

2013-01-01

380

The role of SNP-loop diuretic interactions in hypertension across ethnic groups in HyperGEN.  

PubMed

Blood pressure (BP) is significantly influenced by genetic factors; however, less than 3% of the BP variance has been accounted for by variants identified from genome-wide association studies (GWAS) of primarily European-descent cohorts. Other genetic influences, including gene-environment (GxE) interactions, may explain more of the unexplained variance in BP. African Americans (AA) have a higher prevalence and earlier age of onset of hypertension (HTN) as compared with European Americans (EA); responses to anti-hypertensive drugs vary across race groups. To examine potential interactions between the use of loop diuretics and HTN traits, we analyzed systolic (SBP) and diastolic (DBP) blood BP from 1222 AA and 1231 EA participants in the Hypertension Genetic Epidemiology Network (HyperGEN). Population-specific score tests were used to test associations of SBP and DBP, using a panel of genotyped and imputed single nucleotide polymorphisms (SNPs) for AA (2.9 million SNPs) and EA (2.3 million SNPs). Several promising loci were identified through gene-loop diuretic interactions, although no SNP reached genome-wide significance after adjustment for genomic inflation. In AA, SNPs in or near the genes NUDT12, CHL1, GRIA1, CACNB2, and PYHIN1 were identified for SBP, and SNPs near ID3 were identified for DBP. For EA, promising SNPs for SBP were identified in ESR1 and for DBP in SPATS2L and EYA2. Among these SNPs, none were common across phenotypes or population groups. Biologic plausibility exists for many of the identified genes, suggesting that these are candidate genes for regulation of BP and/or anti-hypertensive drug response. The lack of genome-wide significance is understandable in this small study employing gene-drug interactions. These findings provide a set of prioritized SNPs/candidate genes for future studies in HTN. Studies in more diversified population samples may help identify previously missed variants. PMID:24400021

de Las Fuentes, Lisa; Sung, Yun Ju; Schwander, Karen L; Kalathiveetil, Sonia; Hunt, Steven C; Arnett, Donna K; Rao, D C

2013-01-01

381

Olivibacter sitiensis gen. nov., sp. nov., isolated from alkaline olive-oil mill wastes in the region of Sitia, Crete.  

PubMed

A novel, Gram-negative, non-motile, non-sporulating, rod-shaped bacterium isolated from a viscous two-phase olive-oil mill waste ('alpeorujo') is described. The strain, designated AW-6T, is an obligate aerobe, forming irregular, pigmented creamy white colonies. The pH and temperature ranges for growth were pH 5-8 and 5-45 degrees C, with optimal pH and temperature for growth of pH 6-7 and 28-32 degrees C, respectively. Strain AW-6T was chemo-organotrophic and utilized mostly D+ -glucose, protocatechuate and D+ -xylose, followed by L-cysteine, D- -fructose, D+ -galactose, L-histidine, lactose, sorbitol and sucrose. Menaquinone-7 was detected in the respiratory chain of strain AW-6T. The major fatty acids of strain AW-6T were C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH, iso-C(15 : 0), iso-C(17 : 0) 3-OH and C(16 : 0). The closest phylogenetic relative of strain AW-6T was clone BIti35 (89.7 % 16S rRNA gene sequence similarity), while Sphingobacterium thalpophilum DSM 11723T was the closest recognized relative within the Sphingobacteriaceae (88.2 % similarity). Strain AW-6T showed a low level of DNA-DNA relatedness to S. thalpophilum DSM 11723T (33.8-37.0 %). The DNA G+C content of strain AW-6T was 45.6 mol%. Physiological and chemotaxonomic data further confirmed the distinctiveness of strain AW-6T from members of the genera Sphingobacterium and Pedobacter. Thus, strain AW-6T is considered to represent a novel species of a new genus within the family Sphingobacteriaceae, for which the name Olivibacter sitiensis gen. nov., sp. nov. is proposed. The type strain is AW-6T =DSM 17696T=CECT 7133T). PMID:17267986

Ntougias, Spyridon; Fasseas, Constantinos; Zervakis, Georgios I

2007-02-01

382

Patients with community acquired pneumonia admitted to European intensive care units: an epidemiological survey of the GenOSept cohort  

PubMed Central

Introduction Community acquired pneumonia (CAP) is the most common infectious reason for admission to the Intensive Care Unit (ICU). The GenOSept study was designed to determine genetic influences on sepsis outcome. Phenotypic data was recorded using a robust clinical database allowing a contemporary analysis of the clinical characteristics, microbiology, outcomes and independent risk factors in patients with severe CAP admitted to ICUs across Europe. Methods Kaplan-Meier analysis was used to determine mortality rates. A Cox Proportional Hazards (PH) model was used to identify variables independently associated with 28-day and six-month mortality. Results Data from 1166 patients admitted to 102 centres across 17 countries was extracted. Median age was 64 years, 62% were male. Mortality rate at 28 days was 17%, rising to 27% at six months. Streptococcus pneumoniae was the commonest organism isolated (28% of cases) with no organism identified in 36%. Independent risk factors associated with an increased risk of death at six months included APACHE II score (hazard ratio, HR, 1.03; confidence interval, CI, 1.01-1.05), bilateral pulmonary infiltrates (HR1.44; CI 1.11-1.87) and ventilator support (HR 3.04; CI 1.64-5.62). Haematocrit, pH and urine volume on day one were all associated with a worse outcome. Conclusions The mortality rate in patients with severe CAP admitted to European ICUs was 27% at six months. Streptococcus pneumoniae was the commonest organism isolated. In many cases the infecting organism was not identified. Ventilator support, the presence of diffuse pulmonary infiltrates, lower haematocrit, urine volume and pH on admission were independent predictors of a worse outcome. PMID:24690444

2014-01-01

383

Paludibaculum fermentans gen. nov., sp. nov., a facultative anaerobe capable of dissimilatory iron reduction from subdivision 3 of the Acidobacteria.  

PubMed

A facultatively anaerobic, non-pigmented, non-spore-forming bacterium was isolated from a littoral wetland of a boreal lake located on Valaam Island, northern Russia, and designated strain P105(T). Cells of this isolate were Gram-negative, non-motile rods coated by S-layers with p2 lattice symmetry. Sugars were the preferred growth substrates. Under anoxic conditions, strain P105(T) was capable of fermentation and dissimilatory Fe(III) reduction. End products of fermentation were acetate, propionate and H2. Strain P105(T) was a mildly acidophilic, mesophilic organism, capable of growth at pH 4.0-7.2 (optimum pH 5.5-6.0) and at 4-35 °C (optimum at 20-28 °C). The major fatty acids were iso-C(15?:?0) and C(16?:?1)?7c; the cells also contained significant amounts of 13,16-dimethyl octacosanedioic acid (isodiabolic acid). The major polar lipids were phosphocholine and phosphoethanolamine; the quinone was MK-8. The G+C content of the DNA was 60.5 mol%. 16S rRNA gene sequence analysis showed that strain P105(T) belongs to subdivision 3 of the Acidobacteria and is only distantly related (90% sequence similarity) to the only currently characterized member of this subdivision, Bryobacter aggregatus. The novel isolate differs from Bryobacter aggregatus in its cell morphology and ability to grow under anoxic conditions and in the presence of iron- and nitrate-reducing capabilities as well as quinone and polar lipid compositions. These differences suggest that strain P105(T) represents a novel genus and species, for which the name Paludibaculum fermentans gen. nov., sp. nov., is proposed. The type strain of Paludibaculum fermentans is P105(T) (?=?DSM 26340(T)?=?VKM B-2878(T)). PMID:24867171

Kulichevskaya, Irina S; Suzina, Natalia E; Rijpstra, W Irene C; Sinninghe Damsté, Jaap S; Dedysh, Svetlana N

2014-08-01

384

Proof-of-Concept of a Networked Validation Environment for Distributed Air/Ground NextGen Concepts  

NASA Technical Reports Server (NTRS)

The National Airspace System (NAS) must be improved to increase capacity, reduce flight delays, and minimize environmental impacts of air travel. NASA has been tasked with aiding the Federal Aviation Administration (FAA) in NAS modernization. Automatic Dependent Surveillance-Broadcast (ADS-B) is an enabling technology that is fundamental to realization of the Next Generation Air Transportation System (NextGen). Despite the 2020 FAA mandate requiring ADS-B Out equipage, airspace users are lacking incentives to equip with the requisite ADS-B avionics. A need exists to validate in flight tests advanced concepts of operation (ConOps) that rely on ADS-B and other data links without requiring costly equipage. A potential solution is presented in this paper. It is possible to emulate future data link capabilities using the existing in-flight Internet and reduced-cost test equipment. To establish proof-of-concept, a high-fidelity traffic operations simulation was modified to include a module that simulated Internet transmission of ADS-B messages. An advanced NASA ConOp, Flight Deck Interval Management (FIM), was used to evaluate technical feasibility. A preliminary assessment of the effects of latency and dropout rate on FIM was performed. Flight hardware that would be used by proposed test environment was connected to the simulation so that data transfer from aircraft systems to test equipment could be verified. The results indicate that the FIM ConOp, and therefore, many other advanced ConOps with equal or lesser response characteristics and data requirements, can be evaluated in flight using the proposed concept.

Grisham, James; Larson, Natalie; Nelson, Justin; Reed, Joshua; Suggs, Marvin; Underwood, Matthew; Papelis, Yiannis; Ballin, Mark G.

2013-01-01

385

Aquimonas voraii gen. nov., sp. nov., a novel gammaproteobacterium isolated from a warm spring of Assam, India.  

PubMed

A bacterial strain designated GPTSA 20(T), which was isolated from a warm spring in Assam, India, was characterized by using a polyphasic approach. The cells were Gram-negative, aerobic rods, which could not utilize or produce acid from most of the carbohydrates tested. The predominant fatty acids were C(15:0) iso (25.04%), C(17:1) iso omega9c (19.28%), C(16:0) iso (17.73%) and C(11:0) iso 3-OH (9.34%). The G+C content was 75 mol%. From 16S rRNA gene sequence analysis (1433 nucleotides, continuous stretch), it was confirmed that strain GPTSA 20(T) belonged to the class 'Gammaproteobacteria'. The closest 16S rRNA gene sequence similarity found (98.2%) was with an uncultured bacterium clone, NB-03 (accession no. AB117707), from an autotrophic nitrifying biofilm. Among culturable bacteria, the closest sequence similarities were with Fulvimonas soli (93.0%), Silanimonas lenta (92.8%), Thermomonas hydrothermalis (92.4%), Frateuria aurantia (91.9%), Rhodanobacter lindaniclasticus (91.9%), Thermomonas haemolytica (91.9%) and Pseudoxanthomonas taiwanensis (91.8%); similarities of less than 91.8% were obtained with other members of the class 'Gammaproteobacteria'. From the biochemical, physiological, chemotaxonomic and phylogenetic analysis, it was clear that strain GPTSA 20(T) was quite different from members of known genera of the class 'Gammaproteobacteria'. Therefore, it is proposed that strain GPTSA 20(T) represents a novel species within a new genus, with the name Aquimonas voraii gen. nov., sp. nov. The type strain is GPTSA 20(T) (=MTCC 6713(T)=JCM 12896(T)). PMID:16014470

Saha, P; Krishnamurthi, S; Mayilraj, S; Prasad, G S; Bora, T C; Chakrabarti, T

2005-07-01

386

GenTAC Registry Report: Gender Differences Among Individuals with Genetically-Triggered Thoracic Aortic Aneurysm and Dissection  

PubMed Central

Previous data suggest women are at increased risk of death from aortic dissection. Therefore, we analyzed data from the GenTAC registry, the NIH-sponsored program that collects information about individuals with genetically-triggered thoracic aortic aneurysms and cardiovascular conditions. We performed cross-sectional analyses in adults with Marfan syndrome (MFS), familial thoracic aortic aneurysm or dissection (FTAAD), bicuspid aortic valve (BAV) with thoracic aortic aneurysm or dissection, and subjects under 50 years of age with thoracic aortic aneurysm or dissection (TAAD<50y). Women comprised 32% of 1449 subjects and were 21% of subjects with BAV, 34% with FTAAD, 22% with TAAD <50y, and 47% with MFS. Thoracic aortic dissections occurred with equal gender frequency yet women with BAV had more extensive dissections. Aortic size was smaller in women but was similar after controlling for BSA. Age at operation for aortic valve dysfunction, aneurysm or dissection did not differ by gender. Multivariate analysis (adjusting for age, BSA, hypertension, study site, diabetes, and subgroup diagnoses) showed that women had fewer total aortic surgeries (OR= 0.65, p < 0.01) and were less likely to receive angiotensin converting enzyme inhibitors (ACEi) (OR=0.68, p < 0.05). As in BAV, other genetically-triggered aortic diseases such as FTAAD and TAAD<50 are more common in males. In women, decreased prevalence of aortic operations and less treatment with ACEi may be due to their smaller absolute aortic diameters. Longitudinal studies are needed to determine if women are at higher risk for adverse events. PMID:23444191

Holmes, Kathryn W.; Maslen, Cheryl L.; Kindem, Mark; Kroner, Barbara L.; Song, Howard K.; Ravekes, William; Dietz, H.C.; Weinsaft, Jonathan W.; Roman, Mary J.; Devereux, Richard B.; Pyeritz, Reed E.; Bavaria, Joseph; Milewski, Karianna; Milewicz, Dianna; LeMaire, Scott A.; Hendershot, Tabitha; Eagle, Kim A.; Tolunay, H. Eser; Desvigne-Nickens, Patrice; Silberbach, Michael

2013-01-01

387

Desulfovirgula thermocuniculi gen. nov., sp. nov., a thermophilic sulfate-reducer isolated from a geothermal underground mine in Japan.  

PubMed

A thermophilic, Gram-positive, endospore-forming, sulfate-reducing bacterial strain, designated RL80JIV(T), was isolated from a geothermally active underground mine in Japan. Cells were rod-shaped and motile. The temperature and pH ranges for growth were 61-80 degrees C (optimum at 69-72 degrees C) and pH 6.4-7.9 (optimum at pH 6.8-7.3), and the strain tolerated up to 0.5 % NaCl. Strain RL80JIV(T) utilized sulfate, sulfite, thiosulfate and elemental sulfur as electron acceptors. Electron donors utilized were H(2) in the presence of CO(2), and carboxylic acids. Fermentative growth occurred on lactate and pyruvate. The cell wall contained meso-diaminopimelic acid and the major respiratory isoprenoid quinone was menaquinone MK-7. Major whole-cell fatty acids were iso-C(15 : 0), iso-C(17 : 0) and C(16 : 0). Strain RL80JIV(T) was found to be affiliated with the thiosulfate-reducer Thermanaeromonas toyohensis DSM 14490(T) (90.9 % 16S rRNA gene sequence similarity) and with the sulfate-reducer Desulfotomaculum thermocisternum DSM 10259(T) (90.0 % similarity). Strain RL80JIV(T) is therefore considered to represent a novel species of a new genus, for which the name Desulfovirgula thermocuniculi gen. nov., sp. nov. is proposed. The type strain of Desulfovirgula thermocuniculi is RL80JIV(T) (=DSM 16036(T)=JCM 13928(T)). PMID:17220449

Kaksonen, Anna H; Spring, Stefan; Schumann, Peter; Kroppenstedt, Reiner M; Puhakka, Jaakko A

2007-01-01

388

[Geoalkalibacter ferrihydriticus gen. nov., sp. nov., the first alkaliphilic representative of the family Geobacteraceae, isolated from a soda lake].  

PubMed

Investigation of iron reduction in bottom sediments of alkaline soda lakes resulted in the isolation of a new obligately anaerobic iron-reducing bacterium, strain Z-0531, from Lake Khadyn (Tuva Republic, Russia) sediment samples. The cells of strain Z-0531 are short (1.0-1.5 by 0.3-0.5 microm), motile, non-spore-forming, gram-negative rods. The isolate is an obligate alkaliphile, developing in the pH range of 7.8-10.0, with an optimum at pH 8.6. It does not require NaCl but grows at NaCl concentrations of 0-50 g/1l. It can oxidize acetate with such electron acceptors as amorphous Fe(llI) hydroxide (AFH), EDTA-Fe(III), anthraquinone-2,6-disulfonate (quinone), Mn(IV), and S(0). On media with EDTA-Fe(III), the isolate can oxidize, apart from acetate, ethanol, pyruvate, oxalate, arginine, tartrate, lactate, propionate, and serine. H2 is not utilized. The reduced products formed during growth with AFH are siderite or magnetite, depending on the growth conditions. The isolate is incapable of fermenting sugars, peptides, and amino acids. Yeast extract or vitamins are required as growth factors. The organism is capable of dinitrogen fixation and harbors the nifH gene. The DNA G+C content is 55.3 mol %. 16S rRNA analysis places strain Z-0531 into the family Geobacteraceae. Its closest relative (93% similarity) is Desulfuromonas palmitatis. Based on phenotypic distinctions and phylogenetic position, it is proposed that strain Z-0531 be assigned to the new genus and species Geoalkalibacter ferrihydriticus gen. nov., sp. nov. PMID:17205802

Zavarzina, D G; Kolganova, T V; Bulygina, E S; Kostrikina, N A; Turova, T P; Zavarzin, G A

2006-01-01

389

Jatrophihabitans endophyticus gen. nov., sp. nov., an endophytic actinobacterium isolated from a surface-sterilized stem of Jatropha curcas L.  

PubMed

A short rod-shaped Gram-stain-positive actinobacterium was isolated as an endophyte from the tissues of Jatropha curcas cv. KB27 and was investigated by means of a polyphasic taxonomic approach. An analysis of its 16S rRNA gene sequence indicated that strain S9-650(T) forms an individual line of descent and is related to certain members of the suborder Frankineae, order Actinomycetales (<95?% sequence similarity). Distance-matrix and neighbour-joining analyses set the branching point of the novel isolate between two clades, one being represented by members of the genera Frankia (family Frankiaceae) and Acidothermus (family Acidothermaceae) and the other by members of the genera Geodermatophilus, Blastococcus and Modestobacter (family Geodermatophilaceae). The organism had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The acyl type was found to be N-glycolylated. The major menaquinone was MK-9(H4) and the fatty acid profile was characterized by the predominance of iso-C16?:?0, C18?:?1?9c, anteiso-C17?:?0 and C17?:?1?8c. The polar lipids comprised diphosphatidylglycerol, an unidentified glycolipid, phospholipids and aminolipids. The G+C content of the genomic DNA was 71.2 mol%. The distinct phylogenetic position and the phenotypic markers that clearly separate the novel organism from all other members of the suborder Frankineae indicate that strain S9-650(T) represents a novel species in a new genus, for which the name Jatrophihabitans endophyticus gen. nov., sp. nov. is proposed. The type strain of the type species is S9-650(T) (?=?DSM 45627(T)?=?KACC 16232(T)). PMID:22798659

Madhaiyan, Munusamy; Hu, Chuan Jiong; Kim, Soo-Jin; Weon, Hang-Yeon; Kwon, Soon-Wo; Ji, Lianghui

2013-04-01

390

Aliicoccus persicus gen. nov., sp. nov., a halophilic member of the Firmicutes isolated from a hypersaline lake.  

PubMed

A novel Gram-staining-positive, moderately halophilic bacterium, designated strain A76(T), was isolated from a brine sample of the hypersaline lake Aran-Bidgol in Iran. Cells were strictly aerobic, coccus-shaped, non-motile, non-sporulating, and catalase- and oxidase-positive. Strain A76(T) grew between pH 7.0 and 10.0 (optimal growth at pH 8.0), between 20 and 45 °C (optimal growth at 35 °C) and at salinities of 0.5 to 12.5% (w/v) NaCl (optimal growth at 7.5%, w/v, NaCl). On the basis of 16S rRNA gene sequence analysis, strain A76(T) was shown to belong to the phylum Firmicutes with sequence similarities of 94.1, 93.1 and 91.1%, to the type species of the genera Jeotgalicoccus, Salinicoccus and Nosocomiicoccus, respectively. The DNA G+C content of this new isolate was 38.8 mol%. The major cellular fatty acids of strain A76(T) were anteiso-C(15?:?0) and iso-C(15?:?0), and its polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, a glycolipid, an unknown lipid and two unknown phospholipids. The isoprenoid quinones were MK-6 (94%), MK-5 (3%) and MK-7 (3%). The amino acid constituents of the cell wall were Lys, Asp, Gly, Glu and Ala. The physiological, biochemical and phylogenetic differences between strain A76(T) and type strains of taxa with validly published names suggest that this strain represents a novel species in a novel genus within the family Staphylococcaceae, for which the name Aliicoccus persicus gen. nov., sp. nov. is proposed. The type strain of Aliicoccus persicus is strain A76(T) (?=?CECT 8508(T)?=?DSM 28306(T)?=?IBRC-M 10081(T)). PMID:24599898

Amoozegar, Mohammad Ali; Bagheri, Maryam; Makhdoumi-Kakhki, Ali; Didari, Maryam; Schumann, Peter; Nikou, Mahdi Moshtaghi; Sánchez-Porro, Cristina; Ventosa, Antonio

2014-06-01

391

Wenyingzhuangia marina gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from a recirculating mariculture system.  

PubMed

A Gram-stain-negative, strictly aerobic and heterotrophic bacterial strain, designed strain D1(T), was isolated from a recirculating mariculture system in Tianjin, China. Its taxonomic position was determined using a polyphasic approach. Cells of strain D1(T) were non-flagellated short rods, 0.3-0.5 µm wide and 0.5-1.0 µm long. Growth was observed at 15-30 °C (optimum, 25 °C), at pH 5.5-9.0 (optimum, pH 6.5-7.0) and in the presence of 1-8% (w/v) NaCl (optimum, 2-3 %). Cells contained carotenoid pigments but not flexirubin-type pigments. Strain D1(T) contained MK-6 as the sole menaquinone and phosphatidylethanolamine (PE) as the sole phospholipid and four unidentified lipids. The major cellular fatty acids (>10%) were iso-C15 : 0 (23.2 %), iso-C17 : 0 3-OH (15.2%), C(16 : 1)?7c/C(16 : 1)?6c (14.3%), iso-C(15 : 0) 3-OH (13.5%) and iso-C15 : 1 G (10.8%). 16S rRNA gene sequence analyses indicated that strain D1(T) belonged to the family Flavobacteriaceae and showed closest phylogenetic relationship to the genus Lutibacter, with highest sequence similarity to Lutibacter aestuarii MA-My1(T) (92.2%). The DNA G+C content of strain D1(T) was 35.9 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain D1(T) was considered to represent a novel species in a new genus of the family Flavobacteriaceae, for which the name Wenyingzhuangia marina gen. nov., sp. nov. is proposed. The type strain of the type species is D1(T) (?=?CGMCC 1.12162(T)?=?JCM 18494(T)). PMID:24096358

Liu, Ying; Liu, Liang-Zi; Liu, Hong-Can; Zhou, Yu-Guang; Qi, Fang-Jun; Liu, Zhi-Pei

2014-02-01

392

Lutimonas vermicola gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from the marine polychaete Periserrula leucophryna.  

PubMed

A Gram-negative, yellow-coloured, non-motile, chemoheterotrophic, strictly aerobic, rod-shaped bacterium, designated IMCC1616(T), was isolated from the marine polychaete Periserrula leucophryna inhabiting tidal flat sediment of the Yellow Sea, and characterized by a polyphasic approach. The temperature, pH and NaCl ranges for growth were 3-37 degrees C, pH 5.0-11.0 and 0.5-7.5 %. Based on 16S rRNA gene sequence similarity analyses, the strain was most closely related to members of the genera Lutibacter (90.7 %), Tenacibaculum (89.2-90.4 %) and Polaribacter (88.4-90.2 %). Phylogenetic analysis using three treeing algorithms based on 16S rRNA gene sequences indicated that the strain formed a distinct lineage within the family Flavobacteriaceae. The DNA G+C content of the strain was 40.1 mol% and the predominant cellular fatty acids were iso-C(15 : 0) (16.5 %), anteiso-C(15 : 0) (10.9 %), iso-C(17 : 0) 3-OH (8.8 %) and iso-C(17 : 1) omega 9c (8.2 %). The DNA G+C content, large amount of iso-C(17 : 1) omega 9c and several phenotypic characteristics, including growth temperature and catalase activity, differentiated the strain from other related genera in the family. Therefore, from the taxonomic evidence collected in this study, it is proposed that strain IMCC1616(T) represents a new genus and species named Lutimonas vermicola gen. nov., sp. nov. The type strain of Lutimonas vermicola is strain IMCC1616(T) (=KCCM 42379(T) =NBRC 102041(T)). PMID:17684236

Yang, Seung-Jo; Choo, Yoe-Jin; Cho, Jang-Cheon

2007-08-01

393

Albirhodobacter marinus gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from sea shore water of Visakhapatnam, India.  

PubMed

A novel marine, Gram-negative, rod-shaped bacterium, designated strain N9(T), was isolated from a water sample of the sea shore at Visakhapatnam, Andhra Pradesh (India). Strain N9(T) was found to be positive for oxidase and catalase activities. The fatty acids were found to be dominated by C(16:0), C(18:1) ?7c and summed in feature 3 (C(16:1) ?7c and/or C(16:1) ?6c). Strain N9(T) was determined to contain Q-10 as the major respiratory quinone and phosphatidylethanolamine, phosphatidylglycerol, two aminophospholipids, two phospholipids and four unidentified lipids as polar lipids. The DNA G+C content of the strain N9(T) was found to be 63 mol%. 16S rRNA gene sequence analysis indicated that Rhodobacter sphaeroides, Rhodobacter johrii, Pseudorhodobacter ferrugineus, Rhodobacter azotoformans, Rhodobacter ovatus and Pseudorhodobacter aquimaris were the nearest phylogenetic neighbours, with pair-wise sequence similarities of 95.43, 95.36, 94.24, 95.31, 95.60 and 94.74 %, respectively. Phylogenetic analysis showed that strain N9(T) formed a distinct branch within the family Rhodobacteraceae and clustered with the clade comprising species of the genus Pseudorhodobacter, together with species of the genera Roseicitreum, Roseinatronobacter, Roseibaca and Rhodobaca. Species of the genus Pseudorhodobacter are phylogenetically close with a 16S rRNA gene sequence dissimilarity of 5.9-7.3 % (92.7-94.1 % similarity). Based on the above-mentioned phenotypic characteristics and on phylogenetic inference, strain N9(T) is proposed as a representative of a new genus and a novel species of the family Rhodobacteraceae as Albirhodobacter marinus gen. nov., sp. nov. The type strain of Albirhodobacter marinus is N9 (= MTCC 11277(T) = JCM 17680(T)). PMID:23001431

Nupur; Vaidya, Bhumika; Tanuku, Naga Radha Srinivas; Pinnaka, Anil Kumar

2013-02-01

394

Roseicitreum antarcticum gen. nov., sp. nov., an aerobic bacteriochlorophyll a-containing alphaproteobacterium isolated from Antarctic sandy intertidal sediment.  

PubMed

A novel Gram-negative, non-motile bacterium, designated strain ZS2-28(T), was isolated from sandy intertidal sediment samples collected from the coastal regions of the Chinese Antarctic Zhongshan Station on the Larsemann Hills, Princess Elizabeth Land, East Antarctica. Strain ZS2-28(T) was obligately heterotrophic, strictly aerobic, psychrotolerant (growth occurred at 0-33 °C) and moderately halophilic (optimal growth in 7-8?% NaCl). A single major peak at 872-874 nm in the infrared absorption spectrum indicated the presence of bacteriochlorophyll a. Poly-?-hydroxybutyrate accumulation and slime production were also detected. The predominant cellular fatty acid was C??:??7c, with C??:? 3-OH, C??:?, C??:? cyclo, C??:??8c cyclo and summed feature 3 (C??:??7c and/or iso-C??:? 2-OH) present in smaller amounts. The respiratory quinone was Q-10. The main polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified aminolipid. The G+C content of the genomic DNA was 63.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain ZS2-28(T) formed a distinct evolutionary lineage within the clade containing members of the genera Roseibaca, Roseinatronobacter and Rhodobaca of the class Alphaproteobacteria. On the basis of its phylogenetic position, as well as its phenotypic and chemotaxonomic characteristics, strain ZS2-28(T) represents a novel species of a novel genus, for which the name Roseicitreum antarcticum gen. nov., sp. nov. is proposed. The type strain is ZS2-28(T) (?=?CGMCC 1.8894(T) ?=?LMG 24863(T)). PMID:20889763

Yu, Yong; Yan, Shu-Lin; Li, Hui-Rong; Zhang, Xiao-Hua

2011-09-01

395

Roseibaca ekhonensis gen. nov., sp. nov., an alkalitolerant and aerobic bacteriochlorophyll a-producing alphaproteobacterium from hypersaline Ekho Lake.  

PubMed

A Gram-negative, aerobic rod was isolated from the hypersaline, heliothermal and meromictic Ekho Lake (East Antarctica) at a depth of 6 m. The novel strain (designated EL-50T) was oxidase-positive and weakly catalase-positive and metabolized a variety of carboxylic acids, alcohols, sugars and lipids. Cells of strain EL-50T had an absolute requirement for artificial seawater or NaCl. Optimum growth occurred at 16 degrees C and at pH values ranging from 7.0 to 9.5. A large in vivo absorption band at 865-866 nm indicated the production of bacteriochlorophyll (bchl) a. The predominant cellular fatty acid of strain EL-50T was 18:1omega7c, with 3-OH 14:1, 16:1omega9c, 16:0 and 18:1omega9c present in lower amounts. Fatty acids 16:0 and 18:1omega9c were probably amide-linked. The main polar lipids were diphosphatidylglycerol, phospatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. Ubiquinone 10 was produced. The cell-wall diamino acid was meso-diaminopimelic acid. The DNA G+C content of strain EL-50T was 61 mol%. 16S rRNA gene sequence comparisons indicated that the novel isolate was phylogenetically most closely related to alkaliphilic Rhodobaca and Roseinatronobacter species (approximately 96% 16S rRNA gene similarity). The organism had no particular relationship to any other cultivated members within the Alphaproteobacteria. The distinct morphological, physiological and genotypic differences from the previously described taxa studied supported the description of a new genus and novel species, for which the name Roseibaca ekhonensis gen. nov., sp. nov. is proposed. The type strain is EL-50T (=DSM 11469T=CECT 7235T). PMID:19567566

Labrenz, Matthias; Lawson, Paul A; Tindall, Brian J; Hirsch, Peter

2009-08-01

396

Arcticibacter svalbardensis gen. nov., sp. nov., of the family Sphingobacteriaceae in the phylum Bacteroidetes, isolated from Arctic soil.  

PubMed

In the course of a study aimed at isolating bacteria from Arctic soils by a method that selectively enriches for rare bioactive actinomycetes, a Gram-stain-negative, pigmented, non-motile rod, designated MN12-7(T), was isolated. The salmon-pink strain was, based on 16S rRNA gene sequence similarity, found to be affiliated with the family Sphingobacteriaceae. Strain MN12-7(T) was catalase-, oxidase- and cellulase-positive and lacked gelatinase, urease, lipase and pectinase. The predominant cellular fatty acids were summed feature 3 (comprising C16?:?1?7c and/or C16?:?1?6c), iso-C15?:?0 and C15?:?1?6c. The major respiratory quinone of strain MN12-7(T) was MK-7, and the major polar lipid was phosphatidylethanolamine in addition to phosphatidylserine, seven unidentified lipids and six unidentified aminolipids. The DNA G+C content of strain MN12-7(T) was 38 mol%. Strain MN12-7(T) formed a separate lineage in a cluster containing 'Candidatus comitans', with which it shared 92.3?% 16S rRNA gene sequence similarity. Based on the phenotypic characteristics and phylogenetic inference, strain MN12-7(T) is proposed as a representative of a novel species in a new genus, Arcticibacter svalbardensis gen. nov., sp. nov. The type strain of the type species is MN12-7(T) (?=?KCTC 32015(T)?=?CIP 110422(T)). PMID:22904219

Prasad, Sathish; Manasa, B Poorna; Buddhi, Sailaja; Pratibha, Mambatta S; Begum, Zareena; Bandi, Sunil; Tirunagari, Preethi; Shivaji, Sisinthy

2013-05-01

397

Lacticigenium naphtae gen. nov., sp. nov., a halotolerant and motile lactic acid bacterium isolated from crude oil.  

PubMed

A novel lactic acid bacterium, strain MIC1-18(T), was isolated from crude oil collected at an oil-water well in Akita, Japan. Cells of strain MIC1-18(T) were found to be facultatively anaerobic, mesophilic, neutrophilic, Gram-negative, non-sporulating, motile by means of peritrichous flagella and oval rods, 1.8-2.5 mum long. Optimum growth was observed at 30 degrees C, pH 7.0 and 3 % (w/v) NaCl. Strain MIC1-18(T) produced acid from l-arabinose, ribose, glucose, fructose, mannose, N-acetylglucosamine, amygdalin, arbutin, salicin, cellobiose, maltose, sucrose, trehalose, gentiobiose and 5-ketogluconate. l-Lactic acid was the major end product from glucose. The major cellular fatty acid was C(16 : 1)omega7c. The cell-wall murein type was A4alpha containing Lys-Glu. The G+C content of the genomic DNA was 37.8 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that strain MIC1-18(T) was accommodated as a member of the lactic acid bacteria of the low-G+C content Gram-positive bacteria; the closest neighbour of this organism was Atopococcus tabaci CCUG 48253(T), with only 90.0 % sequence similarity. On the basis of the phenotypic features and phylogenetic position, a novel genus and species, Lacticigenium naphtae gen. nov., sp. nov., are proposed for strain MIC1-18(T) (=NBRC 101988(T)=DSM 19658(T)). PMID:19329605

Iino, Takao; Suzuki, Ken-Ichiro; Harayama, Shigeaki

2009-04-01

398

A New Troodontid Theropod, Talos sampsoni gen. et sp. nov., from the Upper Cretaceous Western Interior Basin of North America  

PubMed Central

Background Troodontids are a predominantly small-bodied group of feathered theropod dinosaurs notable for their close evolutionary relationship with Avialae. Despite a diverse Asian representation with remarkable growth in recent years, the North American record of the clade remains poor, with only one controversial species—Troodon formosus—presently known from substantial skeletal remains. Methodology/Principal Findings Here we report a gracile new troodontid theropod—Talos sampsoni gen. et sp. nov.—from the Upper Cretaceous Kaiparowits Formation, Utah, USA, representing one of the most complete troodontid skeletons described from North America to date. Histological assessment of the holotype specimen indicates that the adult body size of Talos was notably smaller than that of the contemporary genus Troodon. Phylogenetic analysis recovers Talos as a member of a derived, latest Cretaceous subclade, minimally containing Troodon, Saurornithoides, and Zanabazar. MicroCT scans reveal extreme pathological remodeling on pedal phalanx II-1 of the holotype specimen likely resulting from physical trauma and subsequent infectious processes. Conclusion/Significance Talos sampsoni adds to the singularity of the Kaiparowits Formation dinosaur fauna, which is represented by at least 10 previously unrecognized species including the recently named ceratopsids Utahceratops and Kosmoceratops, the hadrosaurine Gryposaurus monumentensis, the tyrannosaurid Teratophoneus, and the oviraptorosaurian Hagryphus. The presence of a distinct troodontid taxon in the Kaiparowits Formation supports the hypothesis that late Campanian dinosaurs of the Western Interior Basin exhibited restricted geographic ranges and suggests that the taxonomic diversity of Late Cretaceous troodontids from North America is currently underestimated. An apparent traumatic injury to the foot of Talos with evidence of subsequent healing sheds new light on the paleobiology of deinonychosaurians by bolstering functional interpretations of prey grappling and/or intraspecific combat for the second pedal digit, and supporting trackway evidence indicating a minimal role in weight bearing. PMID:21949721

Zanno, Lindsay E.; Varricchio, David J.; O'Connor, Patrick M.; Titus, Alan L.; Knell, Michael J.

2011-01-01

399

Dethiosulfovibrio peptidovorans gen. nov., sp. nov., a new anaerobic, slightly halophilic, thiosulfate-reducing bacterium from corroding offshore oil wells.  

PubMed

A strictly anaerobic thiosulfate-reducing bacterium was isolated from a corroding offshore oil well in Congo and was designated strain SEBR 4207T. Pure culture of the strain induced a very active pitting corrosion of mild steel, with penetration rates of up to 4 mm per year. This constitutes the first experimental evidence of the involvement of thiosulfate reduction in microbial corrosion of steel. Strain SEBR 4207T cells were vibrios (3 to 5 by 1 microns), stained gram negative, and possessed lateral flagella. Spores were not detected. Optimum growth occurred in the presence of 3% NaCl at pH 7.0 and 42 degrees C. Strain SEBR 4207T utilized peptides and amino acids, but not sugars or fatty acids. It fermented serine, histidine, and Casamino Acids, whereas arginine, glutamate, leucine, isoleucine, alanine, valine, methionine, and asparagine were only used in the presence of thiosulfate. Peptides were fermented to acetate, isobutyrate, isovalerate, 2-methylbutyrate, H2, and CO2. The addition of either thiosulfate or sulfur but not sulfate increased peptide utilization, growth rate, and biomass; during growth, H2S was produced and a concomitant decrease in H2 was observed. The addition of either thiosulfate or sulfur also reversed H2 inhibition. 16S rRNA sequence analysis indicates that strain SEBR 4207T is distantly related to members of the genus Thermoanaerobacter (83% similarity). Because the phenotypic and phylogenetic characteristics cannot be assigned to any described genus, strain SEBR 4207T is designated as a new species of a new genus, Dethiosulfovibrio peptidovorans gen. nov., sp. nov. Strain SEBR 4207T has been deposited in the Deutsche Sammlung von Mikroorganismen und zellkulturen GmbH (= DSM 11002). PMID:9226912

Magot, M; Ravot, G; Campaignolle, X; Ollivier, B; Patel, B K; Fardeau, M L; Thomas, P; Crolet, J L; Garcia, J L

1997-07-01

400

Genomic and physiological characterization of the Verrucomicrobia isolate Diplosphaera colitermitum gen. nov., sp. nov., reveals microaerophily and nitrogen fixation genes.  

PubMed

Previously we reported the cultivation of novel verrucomicrobia, including strain TAV2 (93% 16S rRNA gene identity to its nearest cultivated representative, Opitutus terreae PB90-1) from the gut of the termite Reticulitermes flavipes. To gain better insight into the Verrucomicrobia as a whole and understand the role of verrucomicrobia within the termite gut ecosystem, we analyzed a draft genome and undertook a physiological characterization of TAV2. Strain TAV2 is an autochthonous member of the R. flavipes gut microbiota and groups phylogenetically among diverse Verrucomicrobia from R. flavipes and other termites that are represented by 16S rRNA gene sequences alone. TAV2 is a microaerophile, possessing a high-affinity cbb(3)-type terminal oxidase-encoding gene and exhibiting an optimum growth rate between 2 and 8% (vol/vol) oxygen. It has the genetic potential to degrade cellulose, an important function within termite guts, but its in vitro substrate utilization spectrum was limited to starch and a few mono- and disaccharides. Growth occurred on nitrogen-free medium, and genomic screening revealed genes for dinitrogenases, heretofore detected in only a few members of the Verrucomicrobia. This represents the first (i) characterization of a verrucomicrobial species from the termite gut, (ii) report of nif and anf genes in a nonacidophilic verrucomicrobial species, and (iii) description of a microaerophilic genotype and phenotype in this phylum of bacteria. The genetic and physiological distinctiveness of TAV2 supports its recognition as the type strain of a new genus and species, for which the name Diplosphaera colitermitum gen. nov., sp. nov., is proposed. PMID:22194293

Wertz, John T; Kim, Eunji; Breznak, John A; Schmidt, Thomas M; Rodrigues, Jorge L M

2012-03-01

401

Aurantimonas coralicida gen. nov., sp. nov., the causative agent of white plague type II on Caribbean scleractinian corals.  

PubMed

A bacterium previously isolated from a diseased colony of the scleractinian coral Dichocoenia stokesi (common name elliptical star coral) was subjected to a detailed polyphasic taxonomic characterization. The isolate, designated WP1T, was halophilic and strictly aerobic and formed golden-orange-pigmented colonies after prolonged incubation. Cells of WP1T were gram-negative, rod-shaped and showed a characteristic branching rod morphology. Chemotaxonomically, WP1T was characterized by having Q-10 as the major respiratory lipoquinone and sym-homospermidine as the main component of the cellular polyamine content. The predominant constituent in the cellular fatty acid profile was C18:1 omega7c, along with C19:0 cyclo omega8c and C16:0. Other fatty acids present in smaller amounts were C17:0, C18:0, C16:1 omega7c, C20:1 omega7c and C18:1 2-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. Minor amounts of diphosphatidylglycerol, phosphatidylmonomethylethanolamine and phosphatidyldimethylethanolamine were present. The G + C content of the genomic DNA was 66.3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence showed that WP1T represents a separate subline of descent within the order 'Rhizobiales' of the 'Alphaproteobacteria'. The new line of descent falls within the group of families that includes the Rhizobiaceae, Bartonellaceae, Brucellaceae and 'Phyllobacteriaceae', with no particular relative within this group. The 16S rRNA gene sequence similarity to all established taxa within this group was not higher than 92.0% (to Mesorhizobium mediterraneum). To accommodate this emerging coral pathogen, the creation of a new genus and species is proposed, Aurantimonas coralicida gen. nov., sp. nov. (type strain WP1T = CIP 107386T = DSM 14790T). PMID:12892136

Denner, Ewald B M; Smith, Garriet W; Busse, Hans-Jürgen; Schumann, Peter; Narzt, Thomas; Polson, Shawn W; Lubitz, Werner; Richardson, Laurie L

2003-07-01

402

Rasnitsynala sigambrorum gen. et sp. n., a small odonatopterid ("Eomeganisoptera", "Erasipteridae") from the early Late Carboniferous of Hagen-Vorhalle (Germany)  

PubMed Central

Abstract Besides Erasipteroides valentini (Brauckmann in Brauckmann, Koch & Kemper, 1985), Zessinella siope Brauckmann, 1988, and Namurotypus sippeli Brauckmann & Zessin, 1989, Rasnitsynala sigambrorum gen. et sp. n. is the fourth species of the Odonatoptera from the early Late Carboniferous (Early Pennsylvanian: Namurian B, Marsdenian) deposits of the important Hagen-Vorhalle Konservat-Lagerstätte in Germany. With its wing-span of about 55 mm it is unusually small even for the “Eomeganisoptera”. Its venation resembles other small “Eomeganisoptera”, in particular Zessinella siope. This is why it is here assigned to the probably paraphyletic “Erasipteridae” Carpenter, 1939. PMID:22259266

Zessin, Wolfgang; Brauckmann, Carsten; Groning, Elke

2011-01-01

403

Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm.  

PubMed

The taxonomic position of four heterotrophic, aerobic, Gram-negative, non-motile and moderately halophilic marine bacteria, isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm, was established. 16S rDNA sequence analysis indicated that the strains studied are members of the family Flavobacteriaceae, in which they form a distinct lineage. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, the novel bacteria were classified as Mesonia algae gen. nov., sp. nov. The type strain is KMM 3909(T) (=KCTC 12089(T)=CCUG 47092(T)). PMID:14657131

Nedashkovskaya, Olga I; Kim, Seung Bum; Han, Suk Kyun; Lysenko, Anatoly M; Rohde, Manfred; Zhukova, Natalia V; Falsen, Enevold; Frolova, Galina M; Mikhailov, Valery V; Bae, Kyung Sook

2003-11-01

404

Comment on "Position-dependent effective mass Dirac equations with PT- symmetric and non - PT- symmetric potentials" [J. Phys. A: Math. Gen. 39 (2006) 11877--11887  

E-print Network

Jia and Dutra (J. Phys. A: Math. Gen. 39 (2006) 11877) have considered the one-dimensional non-Hermitian complexified potentials with real spectra in the context of position-dependent mass in Dirac equation. In their second example, a smooth step shape mass distribution is considered and a non-Hermitian non - PT- symmetric Lorentz vector potential is obtained. They have mapped this problem into an exactly solvable Rosen-Morse Schrodinger model and claimed that the energy spectrum is real. The energy spectrum they have reported is pure imaginary or at best forms an empty set. Their claim on the reality of the energy spectrum is fragile, therefore.

Omar Mustafa; S. Habib Mazharimousavi

2006-11-30

405

Cicesetrema unami n. gen., n. sp. (Digenea: Cryptogonimidae: Cryptogoniminae) from Paralichthys californicus (Ayres, 1859) (Osteichthyes: Pleuronectiformes: Paralichthydae) in San Quintin Bay, Baja California, Mexico.  

PubMed

Cicesetrema unami n. gen., n. sp. (Digenea: Cryptogonimidae) is described from the intestine of the California halibut, Paralichthys californicus, from San Quintin Bay, Baja California, Mexico. The new genus is distinguished from other members of the Cryptogoniminae in having vitellaria that form asymmetric bunches of follicles and extend in lateral fields from the level of the ovary posteriad beyond the testes. In addition, the species in the new genus possess a subterminal, funnel-shaped oral sucker that is prominent when protruded but usually retracted in a fold at the anterior end. PMID:10647049

Pérez-Ponce de León, G; Castillo-Sanchez, E; Rosales-Casián, J

1999-12-01

406

Effectiveness of a Cloning and Sequencing Exercise on Student Learning with Subsequent Publication in the National Center for Biotechnology Information GenBank  

PubMed Central

With rapid advances in biotechnology and molecular biology, instructors are challenged to not only provide undergraduate students with hands-on experiences in these disciplines but also to engage them in the “real-world” scientific process. Two common topics covered in biotechnology or molecular biology courses are gene-cloning and bioinformatics, but to provide students with a continuous laboratory-based research experience in these techniques is difficult. To meet these challenges, we have partnered with Bio-Rad Laboratories in the development of the “Cloning and Sequencing Explorer Series,” which combines wet-lab experiences (e.g., DNA extraction, polymerase chain reaction, ligation, transformation, and restriction digestion) with bioinformatics analysis (e.g., evaluation of DNA sequence quality, sequence editing, Basic Local Alignment Search Tool searches, contig construction, intron identification, and six-frame translation) to produce a sequence publishable in the National Center for Biotechnology Information GenBank. This 6- to 8-wk project-based exercise focuses on a pivotal gene of glycolysis (glyceraldehyde-3-phosphate dehydrogenase), in which students isolate, sequence, and characterize the gene from a plant species or cultivar not yet published in GenBank. Student achievement was evaluated using pre-, mid-, and final-test assessments, as well as with a survey to assess student perceptions. Student confidence with basic laboratory techniques and knowledge of bioinformatics tools were significantly increased upon completion of this hands-on exercise. PMID:19952101

Lau, Joann M.

2009-01-01

407

Acanoides gen. n., a new spider genus from China with a note on the taxonomic status of Acanthoneta Eskov & Marusik, 1992 (Araneae, Linyphiidae, Micronetinae)  

PubMed Central

Abstract A new “micronetine” genus Acanoides gen. n. is erected to accommodate two species from China: Acanoides beijingensis sp. n. as the type species and Acanoides hengshanensis (Chen & Yin, 2000), comb. n., with the females described for the first time. The genitalic characters and somatic features of the new genus were studied by means of light microscopy and scanning electron microscopy (SEM). The monophyly of the new genus was tested by a phylogenetic analysis based on molecular data. Descriptions of the new genus, the new species and the new combination are presented; SEM images and microscopy pictures of somatic and genitalic characters are provided in detail. To distinguish from other genera with similar genitalic characters, we compare the new genus with the species of Acanthoneta Eskov & Marusik, 1992, Epibellowia Tanasevitch, 1996 and Wubanoides Eskov, 1986. Four putative synapomorphies for Acanoides gen. n. are suggested to support its monophyly that could be tested in the future. Furthermore, redescriptions of the epigynal morphology of Acanthoneta aggressa Chamberlin & Ivie, 1943 (Nearctic) and on the male of A. dokutchaevi Eskov & Marusik, 1993 (Far East Asia, firstly recorded from China) are provided. Based on comparison with Poeciloneta, from which Acanthoneta stat. n. was separated by Saaristo and Tanasevitch (1996), a revised diagnosis is proposed to support the generic status. PMID:24526845

Sun, Ning; Marusik, Yuri M.; Tu, Lihong

2014-01-01

408

Ge Migration Effect of Si/Gen/Si(100) Heterostructure Films Probed by Grazing Incidence Fluorescence X-Ray Absorption Fine Structure  

SciTech Connect

The local structures of Si(20 monolayer)/Gen/Si(100) (n=1, 2, 4 and 8 monolayer) heterostructure films grown by molecular beam epitaxy (MBE) at 400 deg. C are investigated by grazing incidence fluorescence x-ray absorption fine structure. The Ge K-edge EXAFS analysis shows that the local structure of Ge atoms in the 1 or 2 monolayer (ML) Ge heterostructure film where the Ge atoms are dominantly surrounded by Si, is similar to that in Si0.95Ge0.05 alloy. With the thickness of the Ge monolayer increasing to 4 ML, the coordination environment around Ge atoms is close to that of Si70Ge30 alloy. Even for the 8-ML-thick Ge heterostructure film, the fraction of Ge-Si coordination pair in the first shell is as high as 55%, almost the same as that in Si0.50Ge0.50 alloy. These results clearly indicate the Ge migration effect in all Si/Gen/Si(100) heterostructure films, which is due to surface segregation of Ge atoms during growth process caused by large surface mobility of adatoms allowing for decreasing the surface strain.

Pan Zhiyun; Sun Zhihu; Xie Zhi; Fan Jiangwei; Wei Shiqiang [National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230029 (China); Oyanagi, Hiroyuki [National Institute of Advanced Industrial Science and Technology, AIST Tsukuba Central 2, 1-1-1 Umezonoi, Tsukuba, Ibaraki 305-8568 (Japan)

2007-02-02

409

Zebragryllus Desutter-Grandcolas & Cadena-Casteñada, n.gen. a new Gryllinae genus from Eastern and Western Amazonia, South America (Orthoptera, Grylloidea, Gryllidae).  

PubMed

We describe a new genus of grylline cricket, Zebragryllus Desutter-Grandcolas & Cadena-Casteñada n. gen., from the Neotropical Region, using characters of morphology and male genitalia; genitalic characters clearly show that Zebragryllus n. gen. is closely related to Anurogryllus Saussure, 1878. Six species are described as new to science, originating from western (Peru, Colombia) and eastern (French Guiana) Amazonia: Zebragryllus fuscus Desutter-Grandcolas, n. sp., Z. guianensis Desutter-Grandcolas, n. sp., Z. intermedius Desutter-Grandcolas, n. sp., Zebragryllus nauta Desutter-Grandcolas, n. sp., Zebragryllus nouragui Desutter-Grandcolas, n. sp., and Zebragryllus wittoto Desutter-Grandcolas and Cadena-Casteñada, n. sp., type species of the genus. They are characterized by their size, coloration (shining black, most often with white patterns of coloration, hence the genus name), and male and female genitalia. The calling songs of Z. guianensis Desutter-Grandcolas, n. sp., Z. intermedius Desutter-Grandcolas, n. sp., Z. nouragui Desutter-Grandcolas, n. sp., and Z. wittoto Desutter-Grandcolas and Cadena-Casteñada, n. sp. are described. An identification key is proposed for both males and females. PMID:24871163

Desutter-Grandcolas, Laure; Cadena-Castañeda, Oscar J; Jaiswara, Ranjana; Anso, Jeremy

2014-01-01

410

Characterization of Unusual Bacteria Isolated from Respiratory Secretions of Cystic Fibrosis Patients and Description of Inquilinus limosus gen. nov., sp. nov.  

PubMed Central

Using a polyphasic approach (including cellular protein and fatty acid analysis, biochemical characterization, 16S ribosomal DNA sequencing, and DNA-DNA hybridizations), we characterized 51 bacterial isolates recovered from respiratory secretions of cystic fibrosis (CF) patients. Our analyses showed that 24 isolates belong to taxa that have so far not (or only rarely) been reported from CF patients. These taxa include Acinetobacter sp., Bordetella hinzii, Burkholderia fungorum, Comamonas testosteroni, Chryseobacterium sp., Herbaspirillum sp., Moraxella osloensis, Pandoraea genomospecies 4, Ralstonia gilardii, Ralstonia mannitolilytica, Rhizobium radiobacter, and Xanthomonas sp. In addition, one isolate most likely represents a novel Ralstonia species, whereas nine isolates belong to novel taxa within the ?-Proteobacteria. Eight of these latter isolates are classified into the novel genus Inquilinus gen. nov. as Inquilinus limosus gen. nov., sp. nov., or as Inquilinus sp. The remaining 17 isolates are characterized as members of the family Enterobacteriaceae. The recovery of these species suggests that the CF lung is an ecological niche capable of supporting the growth of a wide variety of bacteria rarely seen in clinical samples. Elucidation of the factors that account for the association between these unusual species and the respiratory tract of CF patients may provide important insights into the pathophysiology of CF infection. Because accurate identification of these organisms in the clinical microbiology laboratory may be problematic, the present study highlights the utility of reference laboratories capable of identifying unusual species recovered from CF sputum. PMID:12037065

Coenye, Tom; Goris, Johan; Spilker, Theodore; Vandamme, Peter; LiPuma, John J.

2002-01-01

411

Lucionema balatonense gen. et sp. n., a new nematode of a new family Lucionematidae fam. n. (Dracunculoidea) from the swimbladder of the European pikeperch, Stizostedion lucioperca (Pisces).  

PubMed

A new nematode genus and species, Lucionema balatonense gen. et sp. n., is described from the swimbladder of the European pikeperch, Stizostedion lucioperca (L.), from Lake Balaton in Hungary; a new dracunculoid family Lucionematidae fam. n. is established to accommodate it. The hitherto monotypic family Lucionematidae shows affinities with the families Skrjabillanidae and Daniconematidae, differing from them mainly in having simple oesophagus without external oesophageal glands and the vulva situated near the middle of body; from the first family also in the absence of the buccal capsule and the bursa-like caudal alae in the male. The genus Lucionema gen. n. is characterized mainly by the presence of 8 cephalic papillae in two circlets, absence of spicules, presence of the copulatory plate, only 2 pairs of postanal papillae in the male, and by the distal part of the monodelphic uterus forming a posteriorly directed coil. The body length of L. balatonense females is 1074-1782 microns, that of the only available male 770 microns. A key to the families of the Dracunculoidea is presented. PMID:9516996

Moravec, F; Molnár, K; Székely, C

1998-01-01

412

Morphology and molecular phylogeny of a marine interstitial tetraflagellate with putative endosymbionts: Auranticordis quadriverberis n. gen. et sp. (Cercozoa)  

PubMed Central

Background Comparative morphological studies and environmental sequencing surveys indicate that marine benthic environments contain a diverse assortment of microorganisms that are just beginning to be explored and characterized. The most conspicuous predatory flagellates in these habitats range from about 20–150 ?m in size and fall into three major groups of eukaryotes that are very distantly related to one another: dinoflagellates, euglenids and cercozoans. The Cercozoa is a diverse group of amoeboflagellates that cluster together in molecular phylogenies inferred mainly from ribosomal gene sequences. These molecular phylogenetic studies have demonstrated that several enigmatic taxa, previously treated as Eukaryota insertae sedis, fall within the Cercozoa, and suggest that the actual diversity of this group is largely unknown. Improved knowledge of cercozoan diversity is expected to help resolve major branches in the tree of eukaryotes and demonstrate important cellular innovations for understanding eukaryote evolution. Results A rare tetraflagellate, Auranticordis quadriverberis n. gen. et sp., was isolated from marine sand samples. Uncultured cells were in low abundance and were individually prepared for electron microscopy and DNA sequencing. These flagellates possessed several novel features, such as (1) gliding motility associated with four bundled recurrent flagella, (2) heart-shaped cells about 35–75 ?m in diam., and (3) bright orange coloration caused by linear arrays of muciferous bodies. Each cell also possessed about 2–30 pale orange bodies (usually 4–5 ?m in diam.) that were enveloped by two membranes and sac-like vesicles. The innermost membrane invaginated to form unstacked thylakoids that extended towards a central pyrenoid containing tailed viral particles. Although to our knowledge, these bodies have never been described in any other eukaryote, the ultrastructure was most consistent with photosynthetic endosymbionts of cyanobacterial origin. This combination of morphological features did not allow us to assign A. quadriverberis to any known eukaryotic supergroup. Thus, we sequenced the small subunit rDNA sequence from two different isolates and demonstrated that this lineage evolved from within the Cercozoa. Conclusion Our discovery and characterization of A. quadriverberis underscores how poorly we understand the diversity of cercozoans and, potentially, represents one of the few independent cases of primary endosymbiosis within the Cercozoa and beyond. PMID:18647416

Chantangsi, Chitchai; Esson, Heather J; Leander, Brian S

2008-01-01